>>>>>>>
>>>>>>> INSTALLATION WITH 'R CMD INSTALL --preclean --no-multiarch --library=rMAT.buildbin-libdir rMAT_3.10.0.tar.gz'
>>>>>>>
* installing *source* package 'rMAT' ...
R_HOME: /Library/Frameworks/R.framework/Resources
checking for gcc... clang
checking whether the C compiler works... yes
checking for C compiler default output file name... a.out
checking for suffix of executables...
checking whether we are cross compiling... no
checking for suffix of object files... o
checking whether we are using the GNU C compiler... yes
checking whether clang accepts -g... yes
checking for clang option to accept ISO C89... none needed
checking how to run the C preprocessor... clang -E
checking for pkg-config... /usr/bin/pkg-config
checking pkg-config is at least version 0.9.0... yes
checking for GSL... yes
checking for grep that handles long lines and -e... /usr/bin/grep
checking for egrep... /usr/bin/grep -E
checking for ANSI C header files... rm: conftest.dSYM: is a directory
rm: conftest.dSYM: is a directory
yes
checking for sys/types.h... yes
checking for sys/stat.h... yes
checking for stdlib.h... yes
checking for string.h... yes
checking for memory.h... yes
checking for strings.h... yes
checking for inttypes.h... yes
checking for stdint.h... yes
checking for unistd.h... yes
checking dispatch/dispatch.h usability... yes
checking dispatch/dispatch.h presence... yes
checking for dispatch/dispatch.h... yes
configure: creating ./config.status
config.status: creating src/Makevars
config.status: creating src/config.h
** libs
clang++ -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -I/usr/local/include -fPIC -mtune=native -g -O2 -Wall -pedantic -Wconversion -c BARFileData.cpp -o BARFileData.o
In file included from BARFileData.cpp:20:
./BARFileData.h:205:84: warning: implicit conversion changes signedness: 'int' to 'size_type' (aka 'unsigned long') [-Wsign-conversion]
GDACFILES_BAR_DATA_TYPE GetColumnType(int index) const { return (*m_pColumnTypes)[index]; }
˜ ^˜˜˜˜
./BARFileData.h:223:66: warning: implicit conversion changes signedness: 'int' to 'size_type' (aka 'unsigned long') [-Wsign-conversion]
TagValuePairType &GetParameter(int index) { return m_Parameters[index]; }
˜˜˜˜˜˜˜˜˜˜˜˜ ^˜˜˜˜
./BARFileData.h:410:66: warning: implicit conversion changes signedness: 'int' to 'size_type' (aka 'unsigned long') [-Wsign-conversion]
TagValuePairType &GetParameter(int index) { return m_Parameters[index]; }
˜˜˜˜˜˜˜˜˜˜˜˜ ^˜˜˜˜
./BARFileData.h:416:76: warning: implicit conversion changes signedness: 'int' to 'size_type' (aka 'unsigned long') [-Wsign-conversion]
GDACFILES_BAR_DATA_TYPE &GetColumnTypes(int index) { return m_ColumnTypes[index]; }
˜˜˜˜˜˜˜˜˜˜˜˜˜ ^˜˜˜˜
./BARFileData.h:445:72: warning: implicit conversion changes signedness: 'int' to 'size_type' (aka 'unsigned long') [-Wsign-conversion]
CGDACSequenceResultItem *GetResultsPtr(int index) { return &m_Results[index]; }
˜˜˜˜˜˜˜˜˜ ^˜˜˜˜
BARFileData.cpp:84:54: warning: implicit conversion changes signedness: 'unsigned long' to 'int' [-Wsign-conversion]
int offset = ((iData * GetNumberColumns()) + iCol) * INT_SIZE;
˜˜˜˜˜˜ ˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜^˜˜˜˜˜˜˜˜˜
BARFileData.cpp:84:46: warning: implicit conversion changes signedness: 'int' to 'unsigned long' [-Wsign-conversion]
int offset = ((iData * GetNumberColumns()) + iCol) * INT_SIZE;
˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜^˜˜˜˜˜ ˜
BARFileData.cpp:87:18: warning: implicit conversion changes signedness: 'uint32_t' (aka 'unsigned int') to 'int' [-Wsign-conversion]
data.iValue = MmGetUInt32_N((uint32_t*)(m_lpData + offset));
˜ ^˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜
BARFileData.cpp:140:22: warning: implicit conversion changes signedness: 'int' to 'size_type' (aka 'unsigned long') [-Wsign-conversion]
m_Parameters.resize(m_NumberParameters);
˜˜˜˜˜˜˜˜˜˜˜˜ ^˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜
BARFileData.cpp:141:33: warning: implicit conversion changes signedness: 'int' to 'size_type' (aka 'unsigned long') [-Wsign-conversion]
m_Parameters[m_NumberParameters-1].Tag = tag;
˜˜˜˜˜˜˜˜˜˜˜˜ ˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜^˜
BARFileData.cpp:142:33: warning: implicit conversion changes signedness: 'int' to 'size_type' (aka 'unsigned long') [-Wsign-conversion]
m_Parameters[m_NumberParameters-1].Value = value;
˜˜˜˜˜˜˜˜˜˜˜˜ ˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜^˜
BARFileData.cpp:187:32: warning: implicit conversion changes signedness: 'int' to 'size_type' (aka 'unsigned long') [-Wsign-conversion]
seq.MakeShallowCopy(m_Results[index]);
˜˜˜˜˜˜˜˜˜ ^˜˜˜˜
BARFileData.cpp:283:23: warning: implicit conversion changes signedness: 'int' to 'size_type' (aka 'unsigned long') [-Wsign-conversion]
m_ColumnTypes.resize(m_NumberColumns);
˜˜˜˜˜˜˜˜˜˜˜˜˜ ^˜˜˜˜˜˜˜˜˜˜˜˜˜˜
BARFileData.cpp:287:17: warning: implicit conversion changes signedness: 'int' to 'size_type' (aka 'unsigned long') [-Wsign-conversion]
m_ColumnTypes[i] = (GDACFILES_BAR_DATA_TYPE) cType;
˜˜˜˜˜˜˜˜˜˜˜˜˜ ^
BARFileData.cpp:294:22: warning: implicit conversion changes signedness: 'int' to 'size_type' (aka 'unsigned long') [-Wsign-conversion]
m_Parameters.resize(m_NumberParameters);
˜˜˜˜˜˜˜˜˜˜˜˜ ^˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜
BARFileData.cpp:299:16: warning: implicit conversion changes signedness: 'int' to 'size_type' (aka 'unsigned long') [-Wsign-conversion]
m_Parameters[i].Tag = str;
˜˜˜˜˜˜˜˜˜˜˜˜ ^
BARFileData.cpp:301:16: warning: implicit conversion changes signedness: 'int' to 'size_type' (aka 'unsigned long') [-Wsign-conversion]
m_Parameters[i].Value = str;
˜˜˜˜˜˜˜˜˜˜˜˜ ^
BARFileData.cpp:305:24: warning: implicit conversion loses integer precision: 'streamoff' (aka 'long long') to 'int' [-Wshorten-64-to-32]
m_DataStartPosition = instr.tellg();
˜ ^˜˜˜˜˜˜˜˜˜˜˜˜
BARFileData.cpp:318:23: warning: implicit conversion changes signedness: 'int' to 'size_type' (aka 'unsigned long') [-Wsign-conversion]
m_ColumnTypes.resize(m_NumberColumns);
˜˜˜˜˜˜˜˜˜˜˜˜˜ ^˜˜˜˜˜˜˜˜˜˜˜˜˜˜
BARFileData.cpp:321:25: warning: implicit conversion changes signedness: 'int' to 'size_type' (aka 'unsigned long') [-Wsign-conversion]
switch (m_ColumnTypes[i])
˜˜˜˜˜˜˜˜˜˜˜˜˜ ^
BARFileData.cpp:366:19: warning: implicit conversion changes signedness: 'int' to 'size_type' (aka 'unsigned long') [-Wsign-conversion]
m_Results.resize(m_NumberSequences);
˜˜˜˜˜˜˜˜˜ ^˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜
BARFileData.cpp:371:33: warning: implicit conversion changes signedness: 'int' to 'size_type' (aka 'unsigned long') [-Wsign-conversion]
ReadString_N(instr, m_Results[i].m_Name);
˜˜˜˜˜˜˜˜˜ ^
BARFileData.cpp:374:34: warning: implicit conversion changes signedness: 'int' to 'size_type' (aka 'unsigned long') [-Wsign-conversion]
ReadString_N(instr, m_Results[i].m_GroupName);
˜˜˜˜˜˜˜˜˜ ^
BARFileData.cpp:376:33: warning: implicit conversion changes signedness: 'int' to 'size_type' (aka 'unsigned long') [-Wsign-conversion]
ReadString_N(instr, m_Results[i].m_Version);
˜˜˜˜˜˜˜˜˜ ^
BARFileData.cpp:385:15: warning: implicit conversion changes signedness: 'int' to 'size_type' (aka 'unsigned long') [-Wsign-conversion]
m_Results[i].AddParameter(tag, val);
˜˜˜˜˜˜˜˜˜ ^
BARFileData.cpp:390:13: warning: implicit conversion changes signedness: 'int' to 'size_type' (aka 'unsigned long') [-Wsign-conversion]
m_Results[i].m_NumberDataPoints=cType;
˜˜˜˜˜˜˜˜˜ ^
BARFileData.cpp:391:13: warning: implicit conversion changes signedness: 'int' to 'size_type' (aka 'unsigned long') [-Wsign-conversion]
m_Results[i].m_NumberColumns = m_NumberColumns;
˜˜˜˜˜˜˜˜˜ ^
BARFileData.cpp:392:13: warning: implicit conversion changes signedness: 'int' to 'size_type' (aka 'unsigned long') [-Wsign-conversion]
m_Results[i].m_pColumnTypes = &m_ColumnTypes;
˜˜˜˜˜˜˜˜˜ ^
BARFileData.cpp:393:13: warning: implicit conversion changes signedness: 'int' to 'size_type' (aka 'unsigned long') [-Wsign-conversion]
m_Results[i].m_DataStartPosition = instr.tellg();
˜˜˜˜˜˜˜˜˜ ^
BARFileData.cpp:397:13: warning: implicit conversion changes signedness: 'int' to 'size_type' (aka 'unsigned long') [-Wsign-conversion]
m_Results[i].m_ppData = new BarSequenceResultData *[m_Results[i].m_NumberDataPoints];
˜˜˜˜˜˜˜˜˜ ^
BARFileData.cpp:397:65: warning: implicit conversion changes signedness: 'int' to 'size_type' (aka 'unsigned long') [-Wsign-conversion]
m_Results[i].m_ppData = new BarSequenceResultData *[m_Results[i].m_NumberDataPoints];
˜˜˜˜˜˜˜˜˜ ^
BARFileData.cpp:398:13: warning: implicit conversion changes signedness: 'int' to 'size_type' (aka 'unsigned long') [-Wsign-conversion]
m_Results[i].m_pppData = &m_Results[i].m_ppData;
˜˜˜˜˜˜˜˜˜ ^
BARFileData.cpp:398:39: warning: implicit conversion changes signedness: 'int' to 'size_type' (aka 'unsigned long') [-Wsign-conversion]
m_Results[i].m_pppData = &m_Results[i].m_ppData;
˜˜˜˜˜˜˜˜˜ ^
BARFileData.cpp:399:29: warning: implicit conversion changes signedness: 'int' to 'size_type' (aka 'unsigned long') [-Wsign-conversion]
for (int j=0; j<m_Results[i].m_NumberDataPoints; j++)
˜˜˜˜˜˜˜˜˜ ^
BARFileData.cpp:401:14: warning: implicit conversion changes signedness: 'int' to 'size_type' (aka 'unsigned long') [-Wsign-conversion]
m_Results[i].m_ppData[j] = new BarSequenceResultData[m_NumberColumns];
˜˜˜˜˜˜˜˜˜ ^
BARFileData.cpp:404:23: warning: implicit conversion changes signedness: 'int' to 'size_type' (aka 'unsigned long') [-Wsign-conversion]
if (m_ColumnTypes[k] == BAR_DATA_INTEGER) {
˜˜˜˜˜˜˜˜˜˜˜˜˜ ^
BARFileData.cpp:406:16: warning: implicit conversion changes signedness: 'int' to 'size_type' (aka 'unsigned long') [-Wsign-conversion]
m_Results[i].m_ppData[j][k].iValue = cType;
˜˜˜˜˜˜˜˜˜ ^
BARFileData.cpp:409:35: warning: implicit conversion changes signedness: 'int' to 'size_type' (aka 'unsigned long') [-Wsign-conversion]
ReadFloat_N(instr, m_Results[i].m_ppData[j][k].fValue);
˜˜˜˜˜˜˜˜˜ ^
BARFileData.cpp:393:38: warning: implicit conversion loses integer precision: 'streamoff' (aka 'long long') to 'int' [-Wshorten-64-to-32]
m_Results[i].m_DataStartPosition = instr.tellg();
˜ ^˜˜˜˜˜˜˜˜˜˜˜˜
BARFileData.cpp:578:22: warning: implicit conversion changes signedness: 'int' to 'size_type' (aka 'unsigned long') [-Wsign-conversion]
m_Parameters.resize(m_NumberParameters);
˜˜˜˜˜˜˜˜˜˜˜˜ ^˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜
BARFileData.cpp:579:33: warning: implicit conversion changes signedness: 'int' to 'size_type' (aka 'unsigned long') [-Wsign-conversion]
m_Parameters[m_NumberParameters-1].Tag = tag;
˜˜˜˜˜˜˜˜˜˜˜˜ ˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜^˜
BARFileData.cpp:580:33: warning: implicit conversion changes signedness: 'int' to 'size_type' (aka 'unsigned long') [-Wsign-conversion]
m_Parameters[m_NumberParameters-1].Value = value;
˜˜˜˜˜˜˜˜˜˜˜˜ ˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜^˜
BARFileData.cpp:588:23: warning: implicit conversion changes signedness: 'int' to 'size_type' (aka 'unsigned long') [-Wsign-conversion]
m_ColumnTypes.resize(m_NumberColumns);
˜˜˜˜˜˜˜˜˜˜˜˜˜ ^˜˜˜˜˜˜˜˜˜˜˜˜˜˜
BARFileData.cpp:589:31: warning: implicit conversion changes signedness: 'int' to 'size_type' (aka 'unsigned long') [-Wsign-conversion]
m_ColumnTypes[m_NumberColumns-1] = ctype;
˜˜˜˜˜˜˜˜˜˜˜˜˜ ˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜^˜
BARFileData.cpp:597:19: warning: implicit conversion changes signedness: 'int' to 'size_type' (aka 'unsigned long') [-Wsign-conversion]
m_Results.resize(m_NumberSequences);
˜˜˜˜˜˜˜˜˜ ^˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜
BARFileData.cpp:600:13: warning: implicit conversion changes signedness: 'int' to 'size_type' (aka 'unsigned long') [-Wsign-conversion]
m_Results[i].m_NumberColumns = m_NumberColumns;
˜˜˜˜˜˜˜˜˜ ^
BARFileData.cpp:601:13: warning: implicit conversion changes signedness: 'int' to 'size_type' (aka 'unsigned long') [-Wsign-conversion]
m_Results[i].m_pColumnTypes = &m_ColumnTypes;
˜˜˜˜˜˜˜˜˜ ^
47 warnings generated.
clang++ -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -I/usr/local/include -fPIC -mtune=native -g -O2 -Wall -pedantic -Wconversion -c BARFileWriter.cpp -o BARFileWriter.o
In file included from BARFileWriter.cpp:20:
In file included from ./BARFileWriter.h:34:
./BARFileData.h:205:84: warning: implicit conversion changes signedness: 'int' to 'size_type' (aka 'unsigned long') [-Wsign-conversion]
GDACFILES_BAR_DATA_TYPE GetColumnType(int index) const { return (*m_pColumnTypes)[index]; }
˜ ^˜˜˜˜
./BARFileData.h:223:66: warning: implicit conversion changes signedness: 'int' to 'size_type' (aka 'unsigned long') [-Wsign-conversion]
TagValuePairType &GetParameter(int index) { return m_Parameters[index]; }
˜˜˜˜˜˜˜˜˜˜˜˜ ^˜˜˜˜
./BARFileData.h:410:66: warning: implicit conversion changes signedness: 'int' to 'size_type' (aka 'unsigned long') [-Wsign-conversion]
TagValuePairType &GetParameter(int index) { return m_Parameters[index]; }
˜˜˜˜˜˜˜˜˜˜˜˜ ^˜˜˜˜
./BARFileData.h:416:76: warning: implicit conversion changes signedness: 'int' to 'size_type' (aka 'unsigned long') [-Wsign-conversion]
GDACFILES_BAR_DATA_TYPE &GetColumnTypes(int index) { return m_ColumnTypes[index]; }
˜˜˜˜˜˜˜˜˜˜˜˜˜ ^˜˜˜˜
./BARFileData.h:445:72: warning: implicit conversion changes signedness: 'int' to 'size_type' (aka 'unsigned long') [-Wsign-conversion]
CGDACSequenceResultItem *GetResultsPtr(int index) { return &m_Results[index]; }
˜˜˜˜˜˜˜˜˜ ^˜˜˜˜
BARFileWriter.cpp:100:49: warning: implicit conversion changes signedness: 'int' to 'size_type' (aka 'unsigned long') [-Wsign-conversion]
WriteInt32_N(m_NewBarFile, (int)m_ColumnTypes[i]);
˜˜˜˜˜˜˜˜˜˜˜˜˜ ^
BARFileWriter.cpp:106:44: warning: implicit conversion changes signedness: 'int' to 'size_type' (aka 'unsigned long') [-Wsign-conversion]
WriteString_N(m_NewBarFile, m_Parameters[i].Tag);
˜˜˜˜˜˜˜˜˜˜˜˜ ^
BARFileWriter.cpp:107:44: warning: implicit conversion changes signedness: 'int' to 'size_type' (aka 'unsigned long') [-Wsign-conversion]
WriteString_N(m_NewBarFile, m_Parameters[i].Value);
˜˜˜˜˜˜˜˜˜˜˜˜ ^
BARFileWriter.cpp:113:18: warning: implicit conversion changes signedness: 'int' to 'size_type' (aka 'unsigned long') [-Wsign-conversion]
cout<< m_Results[i].GetName() <<endl;
˜˜˜˜˜˜˜˜˜ ^
BARFileWriter.cpp:114:18: warning: implicit conversion changes signedness: 'int' to 'size_type' (aka 'unsigned long') [-Wsign-conversion]
cout<< m_Results[i].GetGroupName() <<endl;
˜˜˜˜˜˜˜˜˜ ^
BARFileWriter.cpp:115:18: warning: implicit conversion changes signedness: 'int' to 'size_type' (aka 'unsigned long') [-Wsign-conversion]
cout<< m_Results[i].GetVersion() <<endl;
˜˜˜˜˜˜˜˜˜ ^
BARFileWriter.cpp:116:18: warning: implicit conversion changes signedness: 'int' to 'size_type' (aka 'unsigned long') [-Wsign-conversion]
cout<< m_Results[i].GetNumberParameters() <<endl;
˜˜˜˜˜˜˜˜˜ ^
BARFileWriter.cpp:118:41: warning: implicit conversion changes signedness: 'int' to 'size_type' (aka 'unsigned long') [-Wsign-conversion]
WriteString_N(m_NewBarFile, m_Results[i].GetName());
˜˜˜˜˜˜˜˜˜ ^
BARFileWriter.cpp:119:41: warning: implicit conversion changes signedness: 'int' to 'size_type' (aka 'unsigned long') [-Wsign-conversion]
WriteString_N(m_NewBarFile, m_Results[i].GetGroupName());
˜˜˜˜˜˜˜˜˜ ^
BARFileWriter.cpp:120:41: warning: implicit conversion changes signedness: 'int' to 'size_type' (aka 'unsigned long') [-Wsign-conversion]
WriteString_N(m_NewBarFile, m_Results[i].GetVersion());
˜˜˜˜˜˜˜˜˜ ^
BARFileWriter.cpp:121:40: warning: implicit conversion changes signedness: 'int' to 'size_type' (aka 'unsigned long') [-Wsign-conversion]
WriteInt32_N(m_NewBarFile, m_Results[i].GetNumberParameters());
˜˜˜˜˜˜˜˜˜ ^
BARFileWriter.cpp:123:39: warning: implicit conversion changes signedness: 'int' to 'size_type' (aka 'unsigned long') [-Wsign-conversion]
for (int iParam=0; iParam<m_Results[i].GetNumberParameters(); iParam++)
˜˜˜˜˜˜˜˜˜ ^
BARFileWriter.cpp:125:17: warning: implicit conversion changes signedness: 'int' to 'size_type' (aka 'unsigned long') [-Wsign-conversion]
cout<<m_Results[i].GetParameter(iParam).Tag <<endl;
˜˜˜˜˜˜˜˜˜ ^
BARFileWriter.cpp:126:17: warning: implicit conversion changes signedness: 'int' to 'size_type' (aka 'unsigned long') [-Wsign-conversion]
cout<<m_Results[i].GetParameter(iParam).Value <<endl;
˜˜˜˜˜˜˜˜˜ ^
BARFileWriter.cpp:127:42: warning: implicit conversion changes signedness: 'int' to 'size_type' (aka 'unsigned long') [-Wsign-conversion]
WriteString_N(m_NewBarFile, m_Results[i].GetParameter(iParam).Tag);
˜˜˜˜˜˜˜˜˜ ^
BARFileWriter.cpp:128:42: warning: implicit conversion changes signedness: 'int' to 'size_type' (aka 'unsigned long') [-Wsign-conversion]
WriteString_N(m_NewBarFile, m_Results[i].GetParameter(iParam).Value);
˜˜˜˜˜˜˜˜˜ ^
BARFileWriter.cpp:130:40: warning: implicit conversion changes signedness: 'int' to 'size_type' (aka 'unsigned long') [-Wsign-conversion]
WriteInt32_N(m_NewBarFile, m_Results[i].GetNumberDataPoints());
˜˜˜˜˜˜˜˜˜ ^
BARFileWriter.cpp:132:29: warning: implicit conversion changes signedness: 'int' to 'size_type' (aka 'unsigned long') [-Wsign-conversion]
for (int j=0; j<m_Results[i].GetNumberDataPoints(); j++)
˜˜˜˜˜˜˜˜˜ ^
BARFileWriter.cpp:136:15: warning: implicit conversion changes signedness: 'int' to 'size_type' (aka 'unsigned long') [-Wsign-conversion]
m_Results[i].GetData(j,k,data);
˜˜˜˜˜˜˜˜˜ ^
BARFileWriter.cpp:137:23: warning: implicit conversion changes signedness: 'int' to 'size_type' (aka 'unsigned long') [-Wsign-conversion]
if (m_ColumnTypes[k] == BAR_DATA_INTEGER)
˜˜˜˜˜˜˜˜˜˜˜˜˜ ^
25 warnings generated.
clang++ -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -I/usr/local/include -fPIC -mtune=native -g -O2 -Wall -pedantic -Wconversion -c BARReader.cpp -o BARReader.o
In file included from BARReader.cpp:28:
./BARFileData.h:205:84: warning: implicit conversion changes signedness: 'int' to 'size_type' (aka 'unsigned long') [-Wsign-conversion]
GDACFILES_BAR_DATA_TYPE GetColumnType(int index) const { return (*m_pColumnTypes)[index]; }
˜ ^˜˜˜˜
./BARFileData.h:223:66: warning: implicit conversion changes signedness: 'int' to 'size_type' (aka 'unsigned long') [-Wsign-conversion]
TagValuePairType &GetParameter(int index) { return m_Parameters[index]; }
˜˜˜˜˜˜˜˜˜˜˜˜ ^˜˜˜˜
./BARFileData.h:410:66: warning: implicit conversion changes signedness: 'int' to 'size_type' (aka 'unsigned long') [-Wsign-conversion]
TagValuePairType &GetParameter(int index) { return m_Parameters[index]; }
˜˜˜˜˜˜˜˜˜˜˜˜ ^˜˜˜˜
./BARFileData.h:416:76: warning: implicit conversion changes signedness: 'int' to 'size_type' (aka 'unsigned long') [-Wsign-conversion]
GDACFILES_BAR_DATA_TYPE &GetColumnTypes(int index) { return m_ColumnTypes[index]; }
˜˜˜˜˜˜˜˜˜˜˜˜˜ ^˜˜˜˜
./BARFileData.h:445:72: warning: implicit conversion changes signedness: 'int' to 'size_type' (aka 'unsigned long') [-Wsign-conversion]
CGDACSequenceResultItem *GetResultsPtr(int index) { return &m_Results[index]; }
˜˜˜˜˜˜˜˜˜ ^˜˜˜˜
BARReader.cpp:85:24: warning: implicit conversion changes signedness: 'int' to 'size_type' (aka 'unsigned long') [-Wsign-conversion]
m_ColumnTypes.resize (m_NumberColumns);
˜˜˜˜˜˜˜˜˜˜˜˜˜ ^˜˜˜˜˜˜˜˜˜˜˜˜˜˜
BARReader.cpp:91:16: warning: implicit conversion changes signedness: 'int' to 'size_type' (aka 'unsigned long') [-Wsign-conversion]
m_ColumnTypes[i] = (GDACFILES_BAR_DATA_TYPE) cType;
˜˜˜˜˜˜˜˜˜˜˜˜˜ ^
BARReader.cpp:103:23: warning: implicit conversion changes signedness: 'int' to 'size_type' (aka 'unsigned long') [-Wsign-conversion]
m_Parameters.resize (m_NumberParameters);
˜˜˜˜˜˜˜˜˜˜˜˜ ^˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜
BARReader.cpp:111:14: warning: implicit conversion changes signedness: 'int' to 'size_type' (aka 'unsigned long') [-Wsign-conversion]
m_Parameters[i].Tag = str;
˜˜˜˜˜˜˜˜˜˜˜˜ ^
BARReader.cpp:114:14: warning: implicit conversion changes signedness: 'int' to 'size_type' (aka 'unsigned long') [-Wsign-conversion]
m_Parameters[i].Value = str;
˜˜˜˜˜˜˜˜˜˜˜˜ ^
BARReader.cpp:258:6: warning: unused variable 'buf' [-Wunused-variable]
char buf[MAX_SIZE];
^
BARReader.cpp:122:31: warning: implicit conversion loses integer precision: 'streamoff' (aka 'long long') to 'int' [-Wshorten-64-to-32]
int m_DataStartPosition = instr.tellg ();
˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜ ^˜˜˜˜˜˜˜˜˜˜˜˜˜
BARReader.cpp:472:42: warning: unused variable 'regionR' [-Wunused-variable]
SEXP chromosomeR, positionR, matScoreR, regionR, pValueR;
^
BARReader.cpp:473:49: warning: unused variable 'p_region' [-Wunused-variable]
int *p_chromosome = NULL, *p_position = NULL, *p_region = NULL;
^
14 warnings generated.
clang++ -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -I/usr/local/include -fPIC -mtune=native -g -O2 -Wall -pedantic -Wconversion -c BARWriter.cpp -o BARWriter.o
In file included from BARWriter.cpp:30:
In file included from ./BARFileWriter.h:34:
./BARFileData.h:205:84: warning: implicit conversion changes signedness: 'int' to 'size_type' (aka 'unsigned long') [-Wsign-conversion]
GDACFILES_BAR_DATA_TYPE GetColumnType(int index) const { return (*m_pColumnTypes)[index]; }
˜ ^˜˜˜˜
./BARFileData.h:223:66: warning: implicit conversion changes signedness: 'int' to 'size_type' (aka 'unsigned long') [-Wsign-conversion]
TagValuePairType &GetParameter(int index) { return m_Parameters[index]; }
˜˜˜˜˜˜˜˜˜˜˜˜ ^˜˜˜˜
./BARFileData.h:410:66: warning: implicit conversion changes signedness: 'int' to 'size_type' (aka 'unsigned long') [-Wsign-conversion]
TagValuePairType &GetParameter(int index) { return m_Parameters[index]; }
˜˜˜˜˜˜˜˜˜˜˜˜ ^˜˜˜˜
./BARFileData.h:416:76: warning: implicit conversion changes signedness: 'int' to 'size_type' (aka 'unsigned long') [-Wsign-conversion]
GDACFILES_BAR_DATA_TYPE &GetColumnTypes(int index) { return m_ColumnTypes[index]; }
˜˜˜˜˜˜˜˜˜˜˜˜˜ ^˜˜˜˜
./BARFileData.h:445:72: warning: implicit conversion changes signedness: 'int' to 'size_type' (aka 'unsigned long') [-Wsign-conversion]
CGDACSequenceResultItem *GetResultsPtr(int index) { return &m_Results[index]; }
˜˜˜˜˜˜˜˜˜ ^˜˜˜˜
BARWriter.cpp:78:3: warning: control reaches end of non-void function [-Wreturn-type]
}
^
BARWriter.cpp:91:25: warning: unused variable 'startListPtr' [-Wunused-variable]
int curListPtr = 0, startListPtr = 0;
^
BARWriter.cpp:90:10: warning: unused variable 'lengthList' [-Wunused-variable]
int *lengthList = new int[NUM_SEQ];
^
BARWriter.cpp:91:9: warning: unused variable 'curListPtr' [-Wunused-variable]
int curListPtr = 0, startListPtr = 0;
^
BARWriter.cpp:87:9: warning: unused variable 'signal2Length' [-Wunused-variable]
int signal2Length = length(pValue);
^
BARWriter.cpp:92:9: warning: unused variable 'curChromosome' [-Wunused-variable]
int curChromosome = INTEGER(chNos)[0];
^
BARWriter.cpp:93:9: warning: unused variable 'i' [-Wunused-variable]
int i;
^
BARWriter.cpp:181:41: warning: implicit conversion loses floating-point precision: 'double' to 'float' [-Wconversion]
tempStorage[curSeq][i][1].fValue = REAL (MATScores)[curProbePos];
˜ ^˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜
BARWriter.cpp:182:41: warning: implicit conversion loses floating-point precision: 'double' to 'float' [-Wconversion]
tempStorage[curSeq][i][2].fValue = REAL (pValue)[curProbePos];
˜ ^˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜
BARWriter.cpp:277:41: warning: implicit conversion loses floating-point precision: 'double' to 'float' [-Wconversion]
tempStorage[curSeq][i][1].fValue = REAL (normData)[curProbePos];
˜ ^˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜
BARWriter.cpp:271:6: warning: unused variable 'addPos' [-Wunused-variable]
int addPos = 0;
^
16 warnings generated.
clang++ -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -I/usr/local/include -fPIC -mtune=native -g -O2 -Wall -pedantic -Wconversion -c BPMAPFileData.cpp -o BPMAPFileData.o
BPMAPFileData.cpp:127:24: warning: implicit conversion changes signedness: 'int' to 'size_t' (aka 'unsigned long') [-Wsign-conversion]
munmap(m_lpFileMap, m_MapLen);
˜˜˜˜˜˜ ^˜˜˜˜˜˜˜
BPMAPFileData.cpp:304:22: warning: implicit conversion changes signedness: 'uint32_t' (aka 'unsigned int') to 'int' [-Wsign-conversion]
m_NumberSequences = uval;
˜ ^˜˜˜
BPMAPFileData.cpp:308:25: warning: implicit conversion changes signedness: 'int' to 'size_type' (aka 'unsigned long') [-Wsign-conversion]
m_SequenceItems.resize(m_NumberSequences);
˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜ ^˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜
BPMAPFileData.cpp:311:24: warning: implicit conversion loses integer precision: 'streamoff' (aka 'long long') to 'int' [-Wshorten-64-to-32]
m_DataStartPosition = instr.tellg();
˜ ^˜˜˜˜˜˜˜˜˜˜˜˜
BPMAPFileData.cpp:343:46: warning: implicit conversion changes signedness: 'int' to 'size_type' (aka 'unsigned long') [-Wsign-conversion]
ReadUIntLenString_N(instr, m_SequenceItems[iSeq].m_Name);
˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜ ^˜˜˜
BPMAPFileData.cpp:348:20: warning: implicit conversion changes signedness: 'int' to 'size_type' (aka 'unsigned long') [-Wsign-conversion]
m_SequenceItems[iSeq].m_ProbePairs = uval;
˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜ ^˜˜˜
BPMAPFileData.cpp:348:41: warning: implicit conversion changes signedness: 'uint32_t' (aka 'unsigned int') to 'int' [-Wsign-conversion]
m_SequenceItems[iSeq].m_ProbePairs = uval;
˜ ^˜˜˜
BPMAPFileData.cpp:350:20: warning: implicit conversion changes signedness: 'int' to 'size_type' (aka 'unsigned long') [-Wsign-conversion]
m_SequenceItems[iSeq].m_HitStartPosition = uval;
˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜ ^˜˜˜
BPMAPFileData.cpp:350:47: warning: implicit conversion changes signedness: 'uint32_t' (aka 'unsigned int') to 'int' [-Wsign-conversion]
m_SequenceItems[iSeq].m_HitStartPosition = uval;
˜ ^˜˜˜
BPMAPFileData.cpp:354:19: warning: implicit conversion changes signedness: 'int' to 'size_type' (aka 'unsigned long') [-Wsign-conversion]
m_SequenceItems[iSeq].m_NumberHits = uval;
˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜ ^˜˜˜
BPMAPFileData.cpp:354:40: warning: implicit conversion changes signedness: 'uint32_t' (aka 'unsigned int') to 'int' [-Wsign-conversion]
m_SequenceItems[iSeq].m_NumberHits = uval;
˜ ^˜˜˜
BPMAPFileData.cpp:358:47: warning: implicit conversion changes signedness: 'int' to 'size_type' (aka 'unsigned long') [-Wsign-conversion]
ReadUIntLenString_N(instr, m_SequenceItems[iSeq].m_GroupName);
˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜ ^˜˜˜
BPMAPFileData.cpp:359:47: warning: implicit conversion changes signedness: 'int' to 'size_type' (aka 'unsigned long') [-Wsign-conversion]
ReadUIntLenString_N(instr, m_SequenceItems[iSeq].m_SeqVersion);
˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜ ^˜˜˜
BPMAPFileData.cpp:362:20: warning: implicit conversion changes signedness: 'int' to 'size_type' (aka 'unsigned long') [-Wsign-conversion]
m_SequenceItems[iSeq].m_Parameters.resize(uval);
˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜ ^˜˜˜
BPMAPFileData.cpp:365:48: warning: implicit conversion changes signedness: 'int' to 'size_type' (aka 'unsigned long') [-Wsign-conversion]
ReadUIntLenString_N(instr, m_SequenceItems[iSeq].m_Parameters[iParam].Tag);
˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜ ^˜˜˜
BPMAPFileData.cpp:365:67: warning: implicit conversion changes signedness: 'int' to 'size_type' (aka 'unsigned long') [-Wsign-conversion]
ReadUIntLenString_N(instr, m_SequenceItems[iSeq].m_Parameters[iParam].Tag);
˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜ ^˜˜˜˜˜
BPMAPFileData.cpp:366:48: warning: implicit conversion changes signedness: 'int' to 'size_type' (aka 'unsigned long') [-Wsign-conversion]
ReadUIntLenString_N(instr, m_SequenceItems[iSeq].m_Parameters[iParam].Value);
˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜ ^˜˜˜
BPMAPFileData.cpp:366:67: warning: implicit conversion changes signedness: 'int' to 'size_type' (aka 'unsigned long') [-Wsign-conversion]
ReadUIntLenString_N(instr, m_SequenceItems[iSeq].m_Parameters[iParam].Value);
˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜ ^˜˜˜˜˜
BPMAPFileData.cpp:379:32: warning: implicit conversion changes signedness: 'int' to 'size_type' (aka 'unsigned long') [-Wsign-conversion]
int hitSize=(m_SequenceItems[iSeq].m_ProbePairs == PM_MM ? HIT_ITEM_SIZE_WITH_PROBE_PAIRS : HIT_ITEM_SIZE_WITH_PM_ONLY);
˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜ ^˜˜˜
BPMAPFileData.cpp:382:33: warning: implicit conversion changes signedness: 'int' to 'size_type' (aka 'unsigned long') [-Wsign-conversion]
instr.seekg(m_SequenceItems[iSeq].m_HitStartPosition);
˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜ ^˜˜˜
BPMAPFileData.cpp:384:21: warning: implicit conversion changes signedness: 'int' to 'size_type' (aka 'unsigned long') [-Wsign-conversion]
m_SequenceItems[iSeq].m_Number = uval;
˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜ ^˜˜˜
BPMAPFileData.cpp:384:38: warning: implicit conversion changes signedness: 'uint32_t' (aka 'unsigned int') to 'int' [-Wsign-conversion]
m_SequenceItems[iSeq].m_Number = uval;
˜ ^˜˜˜
BPMAPFileData.cpp:388:21: warning: implicit conversion changes signedness: 'int' to 'size_type' (aka 'unsigned long') [-Wsign-conversion]
m_SequenceItems[iSeq].m_Number = uval;
˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜ ^˜˜˜
BPMAPFileData.cpp:388:38: warning: implicit conversion changes signedness: 'uint32_t' (aka 'unsigned int') to 'int' [-Wsign-conversion]
m_SequenceItems[iSeq].m_Number = uval;
˜ ^˜˜˜
BPMAPFileData.cpp:389:21: warning: implicit conversion changes signedness: 'int' to 'size_type' (aka 'unsigned long') [-Wsign-conversion]
m_SequenceItems[iSeq].m_HitStartPosition = instr.tellg();
˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜ ^˜˜˜
BPMAPFileData.cpp:394:19: warning: implicit conversion changes signedness: 'int' to 'size_type' (aka 'unsigned long') [-Wsign-conversion]
m_SequenceItems[iSeq].m_Hits.resize(m_SequenceItems[iSeq].m_NumberHits);
˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜ ^˜˜˜
BPMAPFileData.cpp:394:61: warning: implicit conversion changes signedness: 'int' to 'size_type' (aka 'unsigned long') [-Wsign-conversion]
m_SequenceItems[iSeq].m_Hits.resize(m_SequenceItems[iSeq].m_NumberHits);
˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜ ˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜^˜˜˜˜˜˜˜˜˜˜˜
BPMAPFileData.cpp:394:55: warning: implicit conversion changes signedness: 'int' to 'size_type' (aka 'unsigned long') [-Wsign-conversion]
m_SequenceItems[iSeq].m_Hits.resize(m_SequenceItems[iSeq].m_NumberHits);
˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜ ^˜˜˜
BPMAPFileData.cpp:395:19: warning: implicit conversion changes signedness: 'int' to 'size_type' (aka 'unsigned long') [-Wsign-conversion]
m_SequenceItems[iSeq].m_pHits = &m_SequenceItems[iSeq].m_Hits;
˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜ ^˜˜˜
BPMAPFileData.cpp:395:52: warning: implicit conversion changes signedness: 'int' to 'size_type' (aka 'unsigned long') [-Wsign-conversion]
m_SequenceItems[iSeq].m_pHits = &m_SequenceItems[iSeq].m_Hits;
˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜ ^˜˜˜
BPMAPFileData.cpp:398:41: warning: implicit conversion changes signedness: 'int' to 'size_type' (aka 'unsigned long') [-Wsign-conversion]
for (int iHit=0; iHit<m_SequenceItems[iSeq].m_NumberHits; iHit++)
˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜ ^˜˜˜
BPMAPFileData.cpp:401:20: warning: implicit conversion changes signedness: 'int' to 'size_type' (aka 'unsigned long') [-Wsign-conversion]
m_SequenceItems[iSeq].m_Hits[iHit].PMX = uval;
˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜ ^˜˜˜
BPMAPFileData.cpp:401:33: warning: implicit conversion changes signedness: 'int' to 'size_type' (aka 'unsigned long') [-Wsign-conversion]
m_SequenceItems[iSeq].m_Hits[iHit].PMX = uval;
˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜ ^˜˜˜
BPMAPFileData.cpp:403:20: warning: implicit conversion changes signedness: 'int' to 'size_type' (aka 'unsigned long') [-Wsign-conversion]
m_SequenceItems[iSeq].m_Hits[iHit].PMY = uval;
˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜ ^˜˜˜
BPMAPFileData.cpp:403:33: warning: implicit conversion changes signedness: 'int' to 'size_type' (aka 'unsigned long') [-Wsign-conversion]
m_SequenceItems[iSeq].m_Hits[iHit].PMY = uval;
˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜ ^˜˜˜
BPMAPFileData.cpp:404:24: warning: implicit conversion changes signedness: 'int' to 'size_type' (aka 'unsigned long') [-Wsign-conversion]
if (m_SequenceItems[iSeq].m_ProbePairs == PM_MM)
˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜ ^˜˜˜
BPMAPFileData.cpp:407:21: warning: implicit conversion changes signedness: 'int' to 'size_type' (aka 'unsigned long') [-Wsign-conversion]
m_SequenceItems[iSeq].m_Hits[iHit].MMX=uval;
˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜ ^˜˜˜
BPMAPFileData.cpp:407:34: warning: implicit conversion changes signedness: 'int' to 'size_type' (aka 'unsigned long') [-Wsign-conversion]
m_SequenceItems[iSeq].m_Hits[iHit].MMX=uval;
˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜ ^˜˜˜
BPMAPFileData.cpp:409:21: warning: implicit conversion changes signedness: 'int' to 'size_type' (aka 'unsigned long') [-Wsign-conversion]
m_SequenceItems[iSeq].m_Hits[iHit].MMY=uval;
˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜ ^˜˜˜
BPMAPFileData.cpp:409:34: warning: implicit conversion changes signedness: 'int' to 'size_type' (aka 'unsigned long') [-Wsign-conversion]
m_SequenceItems[iSeq].m_Hits[iHit].MMY=uval;
˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜ ^˜˜˜
BPMAPFileData.cpp:411:37: warning: implicit conversion changes signedness: 'int' to 'size_type' (aka 'unsigned long') [-Wsign-conversion]
ReadUInt8(instr, m_SequenceItems[iSeq].m_Hits[iHit].ProbeLength);
˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜ ^˜˜˜
BPMAPFileData.cpp:411:50: warning: implicit conversion changes signedness: 'int' to 'size_type' (aka 'unsigned long') [-Wsign-conversion]
ReadUInt8(instr, m_SequenceItems[iSeq].m_Hits[iHit].ProbeLength);
˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜ ^˜˜˜
BPMAPFileData.cpp:413:88: warning: implicit conversion changes signedness: 'int' to 'size_type' (aka 'unsigned long') [-Wsign-conversion]
byte_to_dna((char *)probeIn, PROBE_STORAGE_BUFFER_LENGTH, probeOut, m_SequenceItems[iSeq].m_Hits[iHit].ProbeLength);
˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜ ^˜˜˜
BPMAPFileData.cpp:413:101: warning: implicit conversion changes signedness: 'int' to 'size_type' (aka 'unsigned long') [-Wsign-conversion]
byte_to_dna((char *)probeIn, PROBE_STORAGE_BUFFER_LENGTH, probeOut, m_SequenceItems[iSeq].m_Hits[iHit].ProbeLength);
˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜ ^˜˜˜
BPMAPFileData.cpp:414:20: warning: implicit conversion changes signedness: 'int' to 'size_type' (aka 'unsigned long') [-Wsign-conversion]
m_SequenceItems[iSeq].m_Hits[iHit].PMProbe = probeOut;
˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜ ^˜˜˜
BPMAPFileData.cpp:414:33: warning: implicit conversion changes signedness: 'int' to 'size_type' (aka 'unsigned long') [-Wsign-conversion]
m_SequenceItems[iSeq].m_Hits[iHit].PMProbe = probeOut;
˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜ ^˜˜˜
BPMAPFileData.cpp:416:52: warning: implicit conversion changes signedness: 'int' to 'size_type' (aka 'unsigned long') [-Wsign-conversion]
ReadFloatFromOldBPMAP_N(instr, m_SequenceItems[iSeq].m_Hits[iHit].MatchScore);
˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜ ^˜˜˜
BPMAPFileData.cpp:416:65: warning: implicit conversion changes signedness: 'int' to 'size_type' (aka 'unsigned long') [-Wsign-conversion]
ReadFloatFromOldBPMAP_N(instr, m_SequenceItems[iSeq].m_Hits[iHit].MatchScore);
˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜ ^˜˜˜
BPMAPFileData.cpp:418:40: warning: implicit conversion changes signedness: 'int' to 'size_type' (aka 'unsigned long') [-Wsign-conversion]
ReadFloat_N(instr, m_SequenceItems[iSeq].m_Hits[iHit].MatchScore);
˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜ ^˜˜˜
BPMAPFileData.cpp:418:53: warning: implicit conversion changes signedness: 'int' to 'size_type' (aka 'unsigned long') [-Wsign-conversion]
ReadFloat_N(instr, m_SequenceItems[iSeq].m_Hits[iHit].MatchScore);
˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜ ^˜˜˜
BPMAPFileData.cpp:420:20: warning: implicit conversion changes signedness: 'int' to 'size_type' (aka 'unsigned long') [-Wsign-conversion]
m_SequenceItems[iSeq].m_Hits[iHit].Position = uval;
˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜ ^˜˜˜
BPMAPFileData.cpp:420:33: warning: implicit conversion changes signedness: 'int' to 'size_type' (aka 'unsigned long') [-Wsign-conversion]
m_SequenceItems[iSeq].m_Hits[iHit].Position = uval;
˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜ ^˜˜˜
BPMAPFileData.cpp:423:20: warning: implicit conversion changes signedness: 'int' to 'size_type' (aka 'unsigned long') [-Wsign-conversion]
m_SequenceItems[iSeq].m_Hits[iHit].TopStrand=uval8;
˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜ ^˜˜˜
BPMAPFileData.cpp:423:33: warning: implicit conversion changes signedness: 'int' to 'size_type' (aka 'unsigned long') [-Wsign-conversion]
m_SequenceItems[iSeq].m_Hits[iHit].TopStrand=uval8;
˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜ ^˜˜˜
BPMAPFileData.cpp:379:7: warning: unused variable 'hitSize' [-Wunused-variable]
int hitSize=(m_SequenceItems[iSeq].m_ProbePairs == PM_MM ? HIT_ITEM_SIZE_WITH_PROBE_PAIRS : HIT_ITEM_SIZE_WITH_PM_ONLY);
^
BPMAPFileData.cpp:389:48: warning: implicit conversion loses integer precision: 'streamoff' (aka 'long long') to 'int' [-Wshorten-64-to-32]
m_SequenceItems[iSeq].m_HitStartPosition = instr.tellg();
˜ ^˜˜˜˜˜˜˜˜˜˜˜˜
BPMAPFileData.cpp:541:38: warning: implicit conversion changes signedness: 'int' to 'size_type' (aka 'unsigned long') [-Wsign-conversion]
seq.MakeShallowCopy(m_SequenceItems[index]);
˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜ ^˜˜˜˜
BPMAPFileData.cpp:587:21: warning: implicit conversion changes signedness: 'int' to 'size_type' (aka 'unsigned long') [-Wsign-conversion]
hit = (*m_pHits)[index];
˜ ^˜˜˜˜
BPMAPFileData.cpp:642:24: warning: implicit conversion changes signedness: 'int' to 'size_type' (aka 'unsigned long') [-Wsign-conversion]
return m_Parameters[index];
˜˜˜˜˜˜˜˜˜˜˜˜ ^˜˜˜˜
59 warnings generated.
clang++ -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -I/usr/local/include -fPIC -mtune=native -g -O2 -Wall -pedantic -Wconversion -c BPMAPfunctions.cpp -o BPMAPfunctions.o
BPMAPfunctions.cpp:322:32: warning: implicit conversion changes signedness: 'unsigned int' to 'int' [-Wsign-conversion]
p_pmx[pos]=hitStorage[pos].PMX;
˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜^˜˜
BPMAPfunctions.cpp:323:39: warning: implicit conversion changes signedness: 'unsigned int' to 'int' [-Wsign-conversion]
p_pmy[pos]=hitStorage[pos].PMY;
˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜^˜˜
BPMAPfunctions.cpp:326:39: warning: implicit conversion changes signedness: 'unsigned int' to 'int' [-Wsign-conversion]
p_mmx[pos]=hitStorage[pos].MMX;
˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜^˜˜
BPMAPfunctions.cpp:327:39: warning: implicit conversion changes signedness: 'unsigned int' to 'int' [-Wsign-conversion]
p_mmy[pos]=hitStorage[pos].MMY;
˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜^˜˜
BPMAPfunctions.cpp:332:58: warning: implicit conversion changes signedness: 'unsigned int' to 'int' [-Wsign-conversion]
if(isPosition){ p_Position[pos]=hitStorage[pos].Position;}
˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜^˜˜˜˜˜˜˜
5 warnings generated.
clang -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -I/usr/local/include -fPIC -mtune=native -g -O2 -Wall -pedantic -Wconversion -c DeclareAll.c -o DeclareAll.o
clang++ -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -I/usr/local/include -fPIC -mtune=native -g -O2 -Wall -pedantic -Wconversion -c FileIO.cpp -o FileIO.o
FileIO.cpp:273:10: warning: implicit conversion changes signedness: 'uint32_t' (aka 'unsigned int') to 'int32_t' (aka 'int') [-Wsign-conversion]
return MmGetUInt32_I((uint32_t*)ptr);
˜˜˜˜˜˜ ^˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜
FileIO.cpp:278:10: warning: implicit conversion changes signedness: 'uint16_t' (aka 'unsigned short') to 'int16_t' (aka 'short') [-Wsign-conversion]
return MmGetUInt16_I((uint16_t*)ptr);
˜˜˜˜˜˜ ^˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜
FileIO.cpp:283:10: warning: implicit conversion changes signedness: 'uint32_t' (aka 'unsigned int') to 'int32_t' (aka 'int') [-Wsign-conversion]
return MmGetUInt32_N((uint32_t*)ptr);
˜˜˜˜˜˜ ^˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜
FileIO.cpp:288:10: warning: implicit conversion changes signedness: 'uint16_t' (aka 'unsigned short') to 'int16_t' (aka 'short') [-Wsign-conversion]
return MmGetUInt16_N((uint16_t*)ptr);
˜˜˜˜˜˜ ^˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜
FileIO.cpp:293:10: warning: implicit conversion changes signedness: 'uint8_t' (aka 'unsigned char') to 'int8_t' (aka 'signed char') [-Wsign-conversion]
return MmGetUInt8((uint8_t*)ptr);
˜˜˜˜˜˜ ^˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜
FileIO.cpp:361:20: warning: implicit conversion changes signedness: 'int' to 'uint32_t' (aka 'unsigned int') [-Wsign-conversion]
uint32_t v=itohl(*(int*)ptr);
˜ ^˜˜˜˜˜˜˜˜˜
./FileIO.h:96:19: note: expanded from macro 'itohl'
#define itohl(x) (x)
^
6 warnings generated.
clang++ -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -I/usr/local/include -fPIC -mtune=native -g -O2 -Wall -pedantic -Wconversion -c FileWriter.cpp -o FileWriter.o
FileWriter.cpp:173:32: warning: implicit conversion changes signedness: 'int' to 'size_t' (aka 'unsigned long') [-Wsign-conversion]
WriteFixedString(outstr, str, len);
˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜ ^˜˜
1 warning generated.
clang -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -I/usr/local/include -fPIC -mtune=native -g -O2 -Wall -pedantic -Wconversion -c NormalizeProbes.c -o NormalizeProbes.o
NormalizeProbes.c:104:59: warning: implicit conversion changes signedness: 'int' to 'size_t' (aka 'unsigned long') [-Wsign-conversion]
copyNumberVector=gsl_vector_view_array(copyNumber,nProbesTotal);
˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜ ^˜˜˜˜˜˜˜˜˜˜˜
NormalizeProbes.c:105:39: warning: implicit conversion changes signedness: 'int' to 'size_t' (aka 'unsigned long') [-Wsign-conversion]
seqNumCount=gsl_matrix_calloc(nProbesTotal,4);
˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜ ^˜˜˜˜˜˜˜˜˜˜˜
NormalizeProbes.c:122:43: warning: implicit conversion changes signedness: 'int' to 'size_t' (aka 'unsigned long') [-Wsign-conversion]
pairNumCount1=gsl_matrix_calloc(nProbesTotal,16);
˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜ ^˜˜˜˜˜˜˜˜˜˜˜
NormalizeProbes.c:123:43: warning: implicit conversion changes signedness: 'int' to 'size_t' (aka 'unsigned long') [-Wsign-conversion]
pairNumCount2=gsl_matrix_calloc(nProbesTotal,16);
˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜ ^˜˜˜˜˜˜˜˜˜˜˜
NormalizeProbes.c:124:43: warning: implicit conversion changes signedness: 'int' to 'size_t' (aka 'unsigned long') [-Wsign-conversion]
pairNumCount3=gsl_matrix_calloc(nProbesTotal,16);
˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜ ^˜˜˜˜˜˜˜˜˜˜˜
NormalizeProbes.c:125:43: warning: implicit conversion changes signedness: 'int' to 'size_t' (aka 'unsigned long') [-Wsign-conversion]
pairNumCount4=gsl_matrix_calloc(nProbesTotal,16);
˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜ ^˜˜˜˜˜˜˜˜˜˜˜
NormalizeProbes.c:142:59: warning: implicit conversion loses integer precision: 'size_t' (aka 'unsigned long') to 'int' [-Wshorten-64-to-32]
yVector, copyNumberVector, jj),
^˜
./config.h:34:45: note: expanded from macro 'DO_NORMALIZE'
^(size_t counter_name) { task; });
^
NormalizeProbes.c:143:26: warning: implicit conversion changes signedness: 'int' to 'size_t' (aka 'unsigned long') [-Wsign-conversion]
jj, *nArrays);
˜˜˜˜^˜˜˜˜˜˜˜˜
./config.h:32:20: note: expanded from macro 'DO_NORMALIZE'
dispatch_apply(n_times, \
^
NormalizeProbes.c:91:13: warning: unused variable 'j' [-Wunused-variable]
int j=0,nVariables;
^
NormalizeProbes.c:171:22: warning: implicit conversion changes signedness: 'int' to 'size_t' (aka 'unsigned long') [-Wsign-conversion]
gsl_matrix_set(X,i,0,1);
˜˜˜˜˜˜˜˜˜˜˜˜˜˜ ^
NormalizeProbes.c:179:26: warning: implicit conversion changes signedness: 'int' to 'size_t' (aka 'unsigned long') [-Wsign-conversion]
gsl_matrix_set(X,i,1+3*j+tempInt-1,1);
˜˜˜˜˜˜˜˜˜˜˜˜˜˜ ^
NormalizeProbes.c:179:41: warning: implicit conversion changes signedness: 'int' to 'size_t' (aka 'unsigned long') [-Wsign-conversion]
gsl_matrix_set(X,i,1+3*j+tempInt-1,1);
˜˜˜˜˜˜˜˜˜˜˜˜˜˜ ˜˜˜˜˜˜˜˜˜˜˜˜˜^˜
NormalizeProbes.c:184:24: warning: implicit conversion changes signedness: 'int' to 'size_t' (aka 'unsigned long') [-Wsign-conversion]
gsl_matrix_set(X,i,1+3*25+j,gsl_pow_2(gsl_matrix_get(seqNumCount,i,j)));
˜˜˜˜˜˜˜˜˜˜˜˜˜˜ ^
NormalizeProbes.c:184:32: warning: implicit conversion changes signedness: 'int' to 'size_t' (aka 'unsigned long') [-Wsign-conversion]
gsl_matrix_set(X,i,1+3*25+j,gsl_pow_2(gsl_matrix_get(seqNumCount,i,j)));
˜˜˜˜˜˜˜˜˜˜˜˜˜˜ ˜˜˜˜˜˜^˜
NormalizeProbes.c:184:72: warning: implicit conversion changes signedness: 'int' to 'size_t' (aka 'unsigned long') [-Wsign-conversion]
gsl_matrix_set(X,i,1+3*25+j,gsl_pow_2(gsl_matrix_get(seqNumCount,i,j)));
˜˜˜˜˜˜˜˜˜˜˜˜˜˜ ^
NormalizeProbes.c:184:74: warning: implicit conversion changes signedness: 'int' to 'size_t' (aka 'unsigned long') [-Wsign-conversion]
gsl_matrix_set(X,i,1+3*25+j,gsl_pow_2(gsl_matrix_get(seqNumCount,i,j)));
˜˜˜˜˜˜˜˜˜˜˜˜˜˜ ^
NormalizeProbes.c:186:22: warning: implicit conversion changes signedness: 'int' to 'size_t' (aka 'unsigned long') [-Wsign-conversion]
gsl_matrix_set(X,i,1+3*25+4,log(gsl_vector_get(copyNumber,i)));
˜˜˜˜˜˜˜˜˜˜˜˜˜˜ ^
NormalizeProbes.c:186:63: warning: implicit conversion changes signedness: 'int' to 'size_t' (aka 'unsigned long') [-Wsign-conversion]
gsl_matrix_set(X,i,1+3*25+4,log(gsl_vector_get(copyNumber,i)));
˜˜˜˜˜˜˜˜˜˜˜˜˜˜ ^
NormalizeProbes.c:165:18: warning: implicit conversion loses integer precision: 'size_t' (aka 'unsigned long') to 'int' [-Wshorten-64-to-32]
int nProbes=X->size1;
˜˜˜˜˜˜˜ ˜˜˜^˜˜˜˜
NormalizeProbes.c:205:40: warning: implicit conversion changes signedness: 'int' to 'size_t' (aka 'unsigned long') [-Wsign-conversion]
gsl_vector_set(XRow,1+3*j+tempInt-1,1);
˜˜˜˜˜˜˜˜˜˜˜˜˜˜ ˜˜˜˜˜˜˜˜˜˜˜˜˜^˜
NormalizeProbes.c:209:31: warning: implicit conversion changes signedness: 'int' to 'size_t' (aka 'unsigned long') [-Wsign-conversion]
gsl_vector_set(XRow,1+3*25+j,gsl_pow_2(gsl_matrix_get(seqNumCount,i,j)));
˜˜˜˜˜˜˜˜˜˜˜˜˜˜ ˜˜˜˜˜˜^˜
NormalizeProbes.c:209:71: warning: implicit conversion changes signedness: 'int' to 'size_t' (aka 'unsigned long') [-Wsign-conversion]
gsl_vector_set(XRow,1+3*25+j,gsl_pow_2(gsl_matrix_get(seqNumCount,i,j)));
˜˜˜˜˜˜˜˜˜˜˜˜˜˜ ^
NormalizeProbes.c:209:73: warning: implicit conversion changes signedness: 'int' to 'size_t' (aka 'unsigned long') [-Wsign-conversion]
gsl_vector_set(XRow,1+3*25+j,gsl_pow_2(gsl_matrix_get(seqNumCount,i,j)));
˜˜˜˜˜˜˜˜˜˜˜˜˜˜ ^
NormalizeProbes.c:211:62: warning: implicit conversion changes signedness: 'int' to 'size_t' (aka 'unsigned long') [-Wsign-conversion]
gsl_vector_set(XRow,1+3*25+4,log(gsl_vector_get(copyNumber,i)));
˜˜˜˜˜˜˜˜˜˜˜˜˜˜ ^
NormalizeProbes.c:299:22: warning: implicit conversion changes signedness: 'int' to 'size_t' (aka 'unsigned long') [-Wsign-conversion]
gsl_matrix_set(X,i,0,1);
˜˜˜˜˜˜˜˜˜˜˜˜˜˜ ^
NormalizeProbes.c:304:24: warning: implicit conversion changes signedness: 'int' to 'size_t' (aka 'unsigned long') [-Wsign-conversion]
gsl_matrix_set(X,i,1+tempInt-1,1);
˜˜˜˜˜˜˜˜˜˜˜˜˜˜ ^
NormalizeProbes.c:304:35: warning: implicit conversion changes signedness: 'int' to 'size_t' (aka 'unsigned long') [-Wsign-conversion]
gsl_matrix_set(X,i,1+tempInt-1,1);
˜˜˜˜˜˜˜˜˜˜˜˜˜˜ ˜˜˜˜˜˜˜˜˜^˜
NormalizeProbes.c:312:26: warning: implicit conversion changes signedness: 'int' to 'size_t' (aka 'unsigned long') [-Wsign-conversion]
gsl_matrix_set(X,i,1+15+12*(j-1)+tempInt-1,1);
˜˜˜˜˜˜˜˜˜˜˜˜˜˜ ^
NormalizeProbes.c:312:49: warning: implicit conversion changes signedness: 'int' to 'size_t' (aka 'unsigned long') [-Wsign-conversion]
gsl_matrix_set(X,i,1+15+12*(j-1)+tempInt-1,1);
˜˜˜˜˜˜˜˜˜˜˜˜˜˜ ˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜^˜
NormalizeProbes.c:319:24: warning: implicit conversion changes signedness: 'int' to 'size_t' (aka 'unsigned long') [-Wsign-conversion]
gsl_matrix_set(X,i,1+15+12*23+j,gsl_pow_2(gsl_matrix_get(seqNumCount,i,j)));
˜˜˜˜˜˜˜˜˜˜˜˜˜˜ ^
NormalizeProbes.c:319:36: warning: implicit conversion changes signedness: 'int' to 'size_t' (aka 'unsigned long') [-Wsign-conversion]
gsl_matrix_set(X,i,1+15+12*23+j,gsl_pow_2(gsl_matrix_get(seqNumCount,i,j)));
˜˜˜˜˜˜˜˜˜˜˜˜˜˜ ˜˜˜˜˜˜˜˜˜˜^˜
NormalizeProbes.c:319:76: warning: implicit conversion changes signedness: 'int' to 'size_t' (aka 'unsigned long') [-Wsign-conversion]
gsl_matrix_set(X,i,1+15+12*23+j,gsl_pow_2(gsl_matrix_get(seqNumCount,i,j)));
˜˜˜˜˜˜˜˜˜˜˜˜˜˜ ^
NormalizeProbes.c:319:78: warning: implicit conversion changes signedness: 'int' to 'size_t' (aka 'unsigned long') [-Wsign-conversion]
gsl_matrix_set(X,i,1+15+12*23+j,gsl_pow_2(gsl_matrix_get(seqNumCount,i,j)));
˜˜˜˜˜˜˜˜˜˜˜˜˜˜ ^
NormalizeProbes.c:320:24: warning: implicit conversion changes signedness: 'int' to 'size_t' (aka 'unsigned long') [-Wsign-conversion]
gsl_matrix_set(X,i,1+15+12*23+4+j,gsl_pow_3(gsl_matrix_get(seqNumCount,i,j)));
˜˜˜˜˜˜˜˜˜˜˜˜˜˜ ^
NormalizeProbes.c:320:38: warning: implicit conversion changes signedness: 'int' to 'size_t' (aka 'unsigned long') [-Wsign-conversion]
gsl_matrix_set(X,i,1+15+12*23+4+j,gsl_pow_3(gsl_matrix_get(seqNumCount,i,j)));
˜˜˜˜˜˜˜˜˜˜˜˜˜˜ ˜˜˜˜˜˜˜˜˜˜˜˜^˜
NormalizeProbes.c:320:78: warning: implicit conversion changes signedness: 'int' to 'size_t' (aka 'unsigned long') [-Wsign-conversion]
gsl_matrix_set(X,i,1+15+12*23+4+j,gsl_pow_3(gsl_matrix_get(seqNumCount,i,j)));
˜˜˜˜˜˜˜˜˜˜˜˜˜˜ ^
NormalizeProbes.c:320:80: warning: implicit conversion changes signedness: 'int' to 'size_t' (aka 'unsigned long') [-Wsign-conversion]
gsl_matrix_set(X,i,1+15+12*23+4+j,gsl_pow_3(gsl_matrix_get(seqNumCount,i,j)));
˜˜˜˜˜˜˜˜˜˜˜˜˜˜ ^
NormalizeProbes.c:323:22: warning: implicit conversion changes signedness: 'int' to 'size_t' (aka 'unsigned long') [-Wsign-conversion]
gsl_matrix_set(X,i,1+15+12*23+8,gsl_vector_get(copyNumber,i));
˜˜˜˜˜˜˜˜˜˜˜˜˜˜ ^
NormalizeProbes.c:323:63: warning: implicit conversion changes signedness: 'int' to 'size_t' (aka 'unsigned long') [-Wsign-conversion]
gsl_matrix_set(X,i,1+15+12*23+8,gsl_vector_get(copyNumber,i));
˜˜˜˜˜˜˜˜˜˜˜˜˜˜ ^
NormalizeProbes.c:292:18: warning: implicit conversion loses integer precision: 'size_t' (aka 'unsigned long') to 'int' [-Wshorten-64-to-32]
int nProbes=X->size1;
˜˜˜˜˜˜˜ ˜˜˜^˜˜˜˜
NormalizeProbes.c:339:34: warning: implicit conversion changes signedness: 'int' to 'size_t' (aka 'unsigned long') [-Wsign-conversion]
gsl_vector_set(XRow,1+tempInt-1,1);
˜˜˜˜˜˜˜˜˜˜˜˜˜˜ ˜˜˜˜˜˜˜˜˜^˜
NormalizeProbes.c:345:48: warning: implicit conversion changes signedness: 'int' to 'size_t' (aka 'unsigned long') [-Wsign-conversion]
gsl_vector_set(XRow,1+15+12*(j-1)+tempInt-1,1);
˜˜˜˜˜˜˜˜˜˜˜˜˜˜ ˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜^˜
NormalizeProbes.c:350:35: warning: implicit conversion changes signedness: 'int' to 'size_t' (aka 'unsigned long') [-Wsign-conversion]
gsl_vector_set(XRow,1+15+12*23+j,gsl_pow_2(gsl_matrix_get(seqNumCount,i,j)));
˜˜˜˜˜˜˜˜˜˜˜˜˜˜ ˜˜˜˜˜˜˜˜˜˜^˜
NormalizeProbes.c:350:75: warning: implicit conversion changes signedness: 'int' to 'size_t' (aka 'unsigned long') [-Wsign-conversion]
gsl_vector_set(XRow,1+15+12*23+j,gsl_pow_2(gsl_matrix_get(seqNumCount,i,j)));
˜˜˜˜˜˜˜˜˜˜˜˜˜˜ ^
NormalizeProbes.c:350:77: warning: implicit conversion changes signedness: 'int' to 'size_t' (aka 'unsigned long') [-Wsign-conversion]
gsl_vector_set(XRow,1+15+12*23+j,gsl_pow_2(gsl_matrix_get(seqNumCount,i,j)));
˜˜˜˜˜˜˜˜˜˜˜˜˜˜ ^
NormalizeProbes.c:351:37: warning: implicit conversion changes signedness: 'int' to 'size_t' (aka 'unsigned long') [-Wsign-conversion]
gsl_vector_set(XRow,1+15+12*23+4+j,gsl_pow_3(gsl_matrix_get(seqNumCount,i,j)));
˜˜˜˜˜˜˜˜˜˜˜˜˜˜ ˜˜˜˜˜˜˜˜˜˜˜˜^˜
NormalizeProbes.c:351:77: warning: implicit conversion changes signedness: 'int' to 'size_t' (aka 'unsigned long') [-Wsign-conversion]
gsl_vector_set(XRow,1+15+12*23+4+j,gsl_pow_3(gsl_matrix_get(seqNumCount,i,j)));
˜˜˜˜˜˜˜˜˜˜˜˜˜˜ ^
NormalizeProbes.c:351:79: warning: implicit conversion changes signedness: 'int' to 'size_t' (aka 'unsigned long') [-Wsign-conversion]
gsl_vector_set(XRow,1+15+12*23+4+j,gsl_pow_3(gsl_matrix_get(seqNumCount,i,j)));
˜˜˜˜˜˜˜˜˜˜˜˜˜˜ ^
NormalizeProbes.c:354:62: warning: implicit conversion changes signedness: 'int' to 'size_t' (aka 'unsigned long') [-Wsign-conversion]
gsl_vector_set(XRow,1+15+12*23+8,gsl_vector_get(copyNumber,i));
˜˜˜˜˜˜˜˜˜˜˜˜˜˜ ^
NormalizeProbes.c:373:22: warning: implicit conversion changes signedness: 'int' to 'size_t' (aka 'unsigned long') [-Wsign-conversion]
gsl_matrix_set(X,i,0,1);
˜˜˜˜˜˜˜˜˜˜˜˜˜˜ ^
NormalizeProbes.c:377:24: warning: implicit conversion changes signedness: 'int' to 'size_t' (aka 'unsigned long') [-Wsign-conversion]
gsl_matrix_set(X,i,1+j,gsl_matrix_get(pairNumCount1,i,j));
˜˜˜˜˜˜˜˜˜˜˜˜˜˜ ^
NormalizeProbes.c:377:27: warning: implicit conversion changes signedness: 'int' to 'size_t' (aka 'unsigned long') [-Wsign-conversion]
gsl_matrix_set(X,i,1+j,gsl_matrix_get(pairNumCount1,i,j));
˜˜˜˜˜˜˜˜˜˜˜˜˜˜ ˜^˜
NormalizeProbes.c:377:59: warning: implicit conversion changes signedness: 'int' to 'size_t' (aka 'unsigned long') [-Wsign-conversion]
gsl_matrix_set(X,i,1+j,gsl_matrix_get(pairNumCount1,i,j));
˜˜˜˜˜˜˜˜˜˜˜˜˜˜ ^
NormalizeProbes.c:377:61: warning: implicit conversion changes signedness: 'int' to 'size_t' (aka 'unsigned long') [-Wsign-conversion]
gsl_matrix_set(X,i,1+j,gsl_matrix_get(pairNumCount1,i,j));
˜˜˜˜˜˜˜˜˜˜˜˜˜˜ ^
NormalizeProbes.c:378:24: warning: implicit conversion changes signedness: 'int' to 'size_t' (aka 'unsigned long') [-Wsign-conversion]
gsl_matrix_set(X,i,1+15+j,gsl_matrix_get(pairNumCount2,i,j));
˜˜˜˜˜˜˜˜˜˜˜˜˜˜ ^
NormalizeProbes.c:378:30: warning: implicit conversion changes signedness: 'int' to 'size_t' (aka 'unsigned long') [-Wsign-conversion]
gsl_matrix_set(X,i,1+15+j,gsl_matrix_get(pairNumCount2,i,j));
˜˜˜˜˜˜˜˜˜˜˜˜˜˜ ˜˜˜˜^˜
NormalizeProbes.c:378:62: warning: implicit conversion changes signedness: 'int' to 'size_t' (aka 'unsigned long') [-Wsign-conversion]
gsl_matrix_set(X,i,1+15+j,gsl_matrix_get(pairNumCount2,i,j));
˜˜˜˜˜˜˜˜˜˜˜˜˜˜ ^
NormalizeProbes.c:378:64: warning: implicit conversion changes signedness: 'int' to 'size_t' (aka 'unsigned long') [-Wsign-conversion]
gsl_matrix_set(X,i,1+15+j,gsl_matrix_get(pairNumCount2,i,j));
˜˜˜˜˜˜˜˜˜˜˜˜˜˜ ^
NormalizeProbes.c:379:24: warning: implicit conversion changes signedness: 'int' to 'size_t' (aka 'unsigned long') [-Wsign-conversion]
gsl_matrix_set(X,i,1+30+j,gsl_matrix_get(pairNumCount3,i,j));
˜˜˜˜˜˜˜˜˜˜˜˜˜˜ ^
NormalizeProbes.c:379:30: warning: implicit conversion changes signedness: 'int' to 'size_t' (aka 'unsigned long') [-Wsign-conversion]
gsl_matrix_set(X,i,1+30+j,gsl_matrix_get(pairNumCount3,i,j));
˜˜˜˜˜˜˜˜˜˜˜˜˜˜ ˜˜˜˜^˜
NormalizeProbes.c:379:62: warning: implicit conversion changes signedness: 'int' to 'size_t' (aka 'unsigned long') [-Wsign-conversion]
gsl_matrix_set(X,i,1+30+j,gsl_matrix_get(pairNumCount3,i,j));
˜˜˜˜˜˜˜˜˜˜˜˜˜˜ ^
NormalizeProbes.c:379:64: warning: implicit conversion changes signedness: 'int' to 'size_t' (aka 'unsigned long') [-Wsign-conversion]
gsl_matrix_set(X,i,1+30+j,gsl_matrix_get(pairNumCount3,i,j));
˜˜˜˜˜˜˜˜˜˜˜˜˜˜ ^
NormalizeProbes.c:380:24: warning: implicit conversion changes signedness: 'int' to 'size_t' (aka 'unsigned long') [-Wsign-conversion]
gsl_matrix_set(X,i,1+45+j,gsl_matrix_get(pairNumCount4,i,j));
˜˜˜˜˜˜˜˜˜˜˜˜˜˜ ^
NormalizeProbes.c:380:30: warning: implicit conversion changes signedness: 'int' to 'size_t' (aka 'unsigned long') [-Wsign-conversion]
gsl_matrix_set(X,i,1+45+j,gsl_matrix_get(pairNumCount4,i,j));
˜˜˜˜˜˜˜˜˜˜˜˜˜˜ ˜˜˜˜^˜
NormalizeProbes.c:380:62: warning: implicit conversion changes signedness: 'int' to 'size_t' (aka 'unsigned long') [-Wsign-conversion]
gsl_matrix_set(X,i,1+45+j,gsl_matrix_get(pairNumCount4,i,j));
˜˜˜˜˜˜˜˜˜˜˜˜˜˜ ^
NormalizeProbes.c:380:64: warning: implicit conversion changes signedness: 'int' to 'size_t' (aka 'unsigned long') [-Wsign-conversion]
gsl_matrix_set(X,i,1+45+j,gsl_matrix_get(pairNumCount4,i,j));
˜˜˜˜˜˜˜˜˜˜˜˜˜˜ ^
NormalizeProbes.c:384:24: warning: implicit conversion changes signedness: 'int' to 'size_t' (aka 'unsigned long') [-Wsign-conversion]
gsl_matrix_set(X,i,1+60+j,gsl_matrix_get(seqNumCount,i,j));
˜˜˜˜˜˜˜˜˜˜˜˜˜˜ ^
NormalizeProbes.c:384:30: warning: implicit conversion changes signedness: 'int' to 'size_t' (aka 'unsigned long') [-Wsign-conversion]
gsl_matrix_set(X,i,1+60+j,gsl_matrix_get(seqNumCount,i,j));
˜˜˜˜˜˜˜˜˜˜˜˜˜˜ ˜˜˜˜^˜
NormalizeProbes.c:384:60: warning: implicit conversion changes signedness: 'int' to 'size_t' (aka 'unsigned long') [-Wsign-conversion]
gsl_matrix_set(X,i,1+60+j,gsl_matrix_get(seqNumCount,i,j));
˜˜˜˜˜˜˜˜˜˜˜˜˜˜ ^
NormalizeProbes.c:384:62: warning: implicit conversion changes signedness: 'int' to 'size_t' (aka 'unsigned long') [-Wsign-conversion]
gsl_matrix_set(X,i,1+60+j,gsl_matrix_get(seqNumCount,i,j));
˜˜˜˜˜˜˜˜˜˜˜˜˜˜ ^
NormalizeProbes.c:387:24: warning: implicit conversion changes signedness: 'int' to 'size_t' (aka 'unsigned long') [-Wsign-conversion]
gsl_matrix_set(X,i,1+63+j,gsl_pow_2(gsl_matrix_get(seqNumCount,i,j)));
˜˜˜˜˜˜˜˜˜˜˜˜˜˜ ^
NormalizeProbes.c:387:30: warning: implicit conversion changes signedness: 'int' to 'size_t' (aka 'unsigned long') [-Wsign-conversion]
gsl_matrix_set(X,i,1+63+j,gsl_pow_2(gsl_matrix_get(seqNumCount,i,j)));
˜˜˜˜˜˜˜˜˜˜˜˜˜˜ ˜˜˜˜^˜
NormalizeProbes.c:387:70: warning: implicit conversion changes signedness: 'int' to 'size_t' (aka 'unsigned long') [-Wsign-conversion]
gsl_matrix_set(X,i,1+63+j,gsl_pow_2(gsl_matrix_get(seqNumCount,i,j)));
˜˜˜˜˜˜˜˜˜˜˜˜˜˜ ^
NormalizeProbes.c:387:72: warning: implicit conversion changes signedness: 'int' to 'size_t' (aka 'unsigned long') [-Wsign-conversion]
gsl_matrix_set(X,i,1+63+j,gsl_pow_2(gsl_matrix_get(seqNumCount,i,j)));
˜˜˜˜˜˜˜˜˜˜˜˜˜˜ ^
NormalizeProbes.c:388:24: warning: implicit conversion changes signedness: 'int' to 'size_t' (aka 'unsigned long') [-Wsign-conversion]
gsl_matrix_set(X,i,1+67+j,gsl_pow_3(gsl_matrix_get(seqNumCount,i,j)));
˜˜˜˜˜˜˜˜˜˜˜˜˜˜ ^
NormalizeProbes.c:388:30: warning: implicit conversion changes signedness: 'int' to 'size_t' (aka 'unsigned long') [-Wsign-conversion]
gsl_matrix_set(X,i,1+67+j,gsl_pow_3(gsl_matrix_get(seqNumCount,i,j)));
˜˜˜˜˜˜˜˜˜˜˜˜˜˜ ˜˜˜˜^˜
NormalizeProbes.c:388:70: warning: implicit conversion changes signedness: 'int' to 'size_t' (aka 'unsigned long') [-Wsign-conversion]
gsl_matrix_set(X,i,1+67+j,gsl_pow_3(gsl_matrix_get(seqNumCount,i,j)));
˜˜˜˜˜˜˜˜˜˜˜˜˜˜ ^
NormalizeProbes.c:388:72: warning: implicit conversion changes signedness: 'int' to 'size_t' (aka 'unsigned long') [-Wsign-conversion]
gsl_matrix_set(X,i,1+67+j,gsl_pow_3(gsl_matrix_get(seqNumCount,i,j)));
˜˜˜˜˜˜˜˜˜˜˜˜˜˜ ^
NormalizeProbes.c:391:22: warning: implicit conversion changes signedness: 'int' to 'size_t' (aka 'unsigned long') [-Wsign-conversion]
gsl_matrix_set(X,i,1+71,gsl_vector_get(copyNumber,i));
˜˜˜˜˜˜˜˜˜˜˜˜˜˜ ^
NormalizeProbes.c:391:55: warning: implicit conversion changes signedness: 'int' to 'size_t' (aka 'unsigned long') [-Wsign-conversion]
gsl_matrix_set(X,i,1+71,gsl_vector_get(copyNumber,i));
˜˜˜˜˜˜˜˜˜˜˜˜˜˜ ^
NormalizeProbes.c:366:18: warning: implicit conversion loses integer precision: 'size_t' (aka 'unsigned long') to 'int' [-Wshorten-64-to-32]
int nProbes=X->size1;
˜˜˜˜˜˜˜ ˜˜˜^˜˜˜˜
NormalizeProbes.c:412:26: warning: implicit conversion changes signedness: 'int' to 'size_t' (aka 'unsigned long') [-Wsign-conversion]
gsl_vector_set(XRow,1+j,gsl_matrix_get(pairNumCount1,i,j));
˜˜˜˜˜˜˜˜˜˜˜˜˜˜ ˜^˜
NormalizeProbes.c:412:58: warning: implicit conversion changes signedness: 'int' to 'size_t' (aka 'unsigned long') [-Wsign-conversion]
gsl_vector_set(XRow,1+j,gsl_matrix_get(pairNumCount1,i,j));
˜˜˜˜˜˜˜˜˜˜˜˜˜˜ ^
NormalizeProbes.c:412:60: warning: implicit conversion changes signedness: 'int' to 'size_t' (aka 'unsigned long') [-Wsign-conversion]
gsl_vector_set(XRow,1+j,gsl_matrix_get(pairNumCount1,i,j));
˜˜˜˜˜˜˜˜˜˜˜˜˜˜ ^
NormalizeProbes.c:413:29: warning: implicit conversion changes signedness: 'int' to 'size_t' (aka 'unsigned long') [-Wsign-conversion]
gsl_vector_set(XRow,1+15+j,gsl_matrix_get(pairNumCount2,i,j));
˜˜˜˜˜˜˜˜˜˜˜˜˜˜ ˜˜˜˜^˜
NormalizeProbes.c:413:61: warning: implicit conversion changes signedness: 'int' to 'size_t' (aka 'unsigned long') [-Wsign-conversion]
gsl_vector_set(XRow,1+15+j,gsl_matrix_get(pairNumCount2,i,j));
˜˜˜˜˜˜˜˜˜˜˜˜˜˜ ^
NormalizeProbes.c:413:63: warning: implicit conversion changes signedness: 'int' to 'size_t' (aka 'unsigned long') [-Wsign-conversion]
gsl_vector_set(XRow,1+15+j,gsl_matrix_get(pairNumCount2,i,j));
˜˜˜˜˜˜˜˜˜˜˜˜˜˜ ^
NormalizeProbes.c:414:29: warning: implicit conversion changes signedness: 'int' to 'size_t' (aka 'unsigned long') [-Wsign-conversion]
gsl_vector_set(XRow,1+30+j,gsl_matrix_get(pairNumCount3,i,j));
˜˜˜˜˜˜˜˜˜˜˜˜˜˜ ˜˜˜˜^˜
NormalizeProbes.c:414:61: warning: implicit conversion changes signedness: 'int' to 'size_t' (aka 'unsigned long') [-Wsign-conversion]
gsl_vector_set(XRow,1+30+j,gsl_matrix_get(pairNumCount3,i,j));
˜˜˜˜˜˜˜˜˜˜˜˜˜˜ ^
NormalizeProbes.c:414:63: warning: implicit conversion changes signedness: 'int' to 'size_t' (aka 'unsigned long') [-Wsign-conversion]
gsl_vector_set(XRow,1+30+j,gsl_matrix_get(pairNumCount3,i,j));
˜˜˜˜˜˜˜˜˜˜˜˜˜˜ ^
NormalizeProbes.c:415:29: warning: implicit conversion changes signedness: 'int' to 'size_t' (aka 'unsigned long') [-Wsign-conversion]
gsl_vector_set(XRow,1+45+j,gsl_matrix_get(pairNumCount4,i,j));
˜˜˜˜˜˜˜˜˜˜˜˜˜˜ ˜˜˜˜^˜
NormalizeProbes.c:415:61: warning: implicit conversion changes signedness: 'int' to 'size_t' (aka 'unsigned long') [-Wsign-conversion]
gsl_vector_set(XRow,1+45+j,gsl_matrix_get(pairNumCount4,i,j));
˜˜˜˜˜˜˜˜˜˜˜˜˜˜ ^
NormalizeProbes.c:415:63: warning: implicit conversion changes signedness: 'int' to 'size_t' (aka 'unsigned long') [-Wsign-conversion]
gsl_vector_set(XRow,1+45+j,gsl_matrix_get(pairNumCount4,i,j));
˜˜˜˜˜˜˜˜˜˜˜˜˜˜ ^
NormalizeProbes.c:419:29: warning: implicit conversion changes signedness: 'int' to 'size_t' (aka 'unsigned long') [-Wsign-conversion]
gsl_vector_set(XRow,1+60+j,gsl_matrix_get(seqNumCount,i,j));
˜˜˜˜˜˜˜˜˜˜˜˜˜˜ ˜˜˜˜^˜
NormalizeProbes.c:419:59: warning: implicit conversion changes signedness: 'int' to 'size_t' (aka 'unsigned long') [-Wsign-conversion]
gsl_vector_set(XRow,1+60+j,gsl_matrix_get(seqNumCount,i,j));
˜˜˜˜˜˜˜˜˜˜˜˜˜˜ ^
NormalizeProbes.c:419:61: warning: implicit conversion changes signedness: 'int' to 'size_t' (aka 'unsigned long') [-Wsign-conversion]
gsl_vector_set(XRow,1+60+j,gsl_matrix_get(seqNumCount,i,j));
˜˜˜˜˜˜˜˜˜˜˜˜˜˜ ^
NormalizeProbes.c:422:29: warning: implicit conversion changes signedness: 'int' to 'size_t' (aka 'unsigned long') [-Wsign-conversion]
gsl_vector_set(XRow,1+63+j,gsl_pow_2(gsl_matrix_get(seqNumCount,i,j)));
˜˜˜˜˜˜˜˜˜˜˜˜˜˜ ˜˜˜˜^˜
NormalizeProbes.c:422:69: warning: implicit conversion changes signedness: 'int' to 'size_t' (aka 'unsigned long') [-Wsign-conversion]
gsl_vector_set(XRow,1+63+j,gsl_pow_2(gsl_matrix_get(seqNumCount,i,j)));
˜˜˜˜˜˜˜˜˜˜˜˜˜˜ ^
NormalizeProbes.c:422:71: warning: implicit conversion changes signedness: 'int' to 'size_t' (aka 'unsigned long') [-Wsign-conversion]
gsl_vector_set(XRow,1+63+j,gsl_pow_2(gsl_matrix_get(seqNumCount,i,j)));
˜˜˜˜˜˜˜˜˜˜˜˜˜˜ ^
NormalizeProbes.c:423:29: warning: implicit conversion changes signedness: 'int' to 'size_t' (aka 'unsigned long') [-Wsign-conversion]
gsl_vector_set(XRow,1+67+j,gsl_pow_3(gsl_matrix_get(seqNumCount,i,j)));
˜˜˜˜˜˜˜˜˜˜˜˜˜˜ ˜˜˜˜^˜
NormalizeProbes.c:423:69: warning: implicit conversion changes signedness: 'int' to 'size_t' (aka 'unsigned long') [-Wsign-conversion]
gsl_vector_set(XRow,1+67+j,gsl_pow_3(gsl_matrix_get(seqNumCount,i,j)));
˜˜˜˜˜˜˜˜˜˜˜˜˜˜ ^
NormalizeProbes.c:423:71: warning: implicit conversion changes signedness: 'int' to 'size_t' (aka 'unsigned long') [-Wsign-conversion]
gsl_vector_set(XRow,1+67+j,gsl_pow_3(gsl_matrix_get(seqNumCount,i,j)));
˜˜˜˜˜˜˜˜˜˜˜˜˜˜ ^
NormalizeProbes.c:426:54: warning: implicit conversion changes signedness: 'int' to 'size_t' (aka 'unsigned long') [-Wsign-conversion]
gsl_vector_set(XRow,1+71,gsl_vector_get(copyNumber,i));
˜˜˜˜˜˜˜˜˜˜˜˜˜˜ ^
NormalizeProbes.c:443:34: warning: implicit conversion changes signedness: 'int' to 'size_t' (aka 'unsigned long') [-Wsign-conversion]
gsl_matrix_set(seqNumCount,i, tempInt-1,gsl_matrix_get(seqNumCount,i,tempInt-1)+1);
˜˜˜˜˜˜˜˜˜˜˜˜˜˜ ^
NormalizeProbes.c:443:44: warning: implicit conversion changes signedness: 'int' to 'size_t' (aka 'unsigned long') [-Wsign-conversion]
gsl_matrix_set(seqNumCount,i, tempInt-1,gsl_matrix_get(seqNumCount,i,tempInt-1)+1);
˜˜˜˜˜˜˜˜˜˜˜˜˜˜ ˜˜˜˜˜˜˜^˜
NormalizeProbes.c:443:74: warning: implicit conversion changes signedness: 'int' to 'size_t' (aka 'unsigned long') [-Wsign-conversion]
gsl_matrix_set(seqNumCount,i, tempInt-1,gsl_matrix_get(seqNumCount,i,tempInt-1)+1);
˜˜˜˜˜˜˜˜˜˜˜˜˜˜ ^
NormalizeProbes.c:443:83: warning: implicit conversion changes signedness: 'int' to 'size_t' (aka 'unsigned long') [-Wsign-conversion]
gsl_matrix_set(seqNumCount,i, tempInt-1,gsl_matrix_get(seqNumCount,i,tempInt-1)+1);
˜˜˜˜˜˜˜˜˜˜˜˜˜˜ ˜˜˜˜˜˜˜^˜
NormalizeProbes.c:432:28: warning: implicit conversion loses integer precision: 'size_t' (aka 'unsigned long') to 'int' [-Wshorten-64-to-32]
int nProbes=seqNumCount->size1;
˜˜˜˜˜˜˜ ˜˜˜˜˜˜˜˜˜˜˜˜˜^˜˜˜˜
NormalizeProbes.c:433:33: warning: implicit conversion loses integer precision: 'size_t' (aka 'unsigned long') to 'int' [-Wshorten-64-to-32]
int nNucleotides=seqNumCount->size2;
˜˜˜˜˜˜˜˜˜˜˜˜ ˜˜˜˜˜˜˜˜˜˜˜˜˜^˜˜˜˜
NormalizeProbes.c:469:36: warning: implicit conversion changes signedness: 'int' to 'size_t' (aka 'unsigned long') [-Wsign-conversion]
gsl_matrix_set(pairNumCount1,i,tempInt-1,gsl_matrix_get(pairNumCount1,i,tempInt-1)+1);
˜˜˜˜˜˜˜˜˜˜˜˜˜˜ ^
NormalizeProbes.c:469:45: warning: implicit conversion changes signedness: 'int' to 'size_t' (aka 'unsigned long') [-Wsign-conversion]
gsl_matrix_set(pairNumCount1,i,tempInt-1,gsl_matrix_get(pairNumCount1,i,tempInt-1)+1);
˜˜˜˜˜˜˜˜˜˜˜˜˜˜ ˜˜˜˜˜˜˜^˜
NormalizeProbes.c:469:77: warning: implicit conversion changes signedness: 'int' to 'size_t' (aka 'unsigned long') [-Wsign-conversion]
gsl_matrix_set(pairNumCount1,i,tempInt-1,gsl_matrix_get(pairNumCount1,i,tempInt-1)+1);
˜˜˜˜˜˜˜˜˜˜˜˜˜˜ ^
NormalizeProbes.c:469:86: warning: implicit conversion changes signedness: 'int' to 'size_t' (aka 'unsigned long') [-Wsign-conversion]
gsl_matrix_set(pairNumCount1,i,tempInt-1,gsl_matrix_get(pairNumCount1,i,tempInt-1)+1);
˜˜˜˜˜˜˜˜˜˜˜˜˜˜ ˜˜˜˜˜˜˜^˜
NormalizeProbes.c:471:36: warning: implicit conversion changes signedness: 'int' to 'size_t' (aka 'unsigned long') [-Wsign-conversion]
gsl_matrix_set(pairNumCount2,i,tempInt-1,gsl_matrix_get(pairNumCount2,i,tempInt-1)+1);
˜˜˜˜˜˜˜˜˜˜˜˜˜˜ ^
NormalizeProbes.c:471:45: warning: implicit conversion changes signedness: 'int' to 'size_t' (aka 'unsigned long') [-Wsign-conversion]
gsl_matrix_set(pairNumCount2,i,tempInt-1,gsl_matrix_get(pairNumCount2,i,tempInt-1)+1);
˜˜˜˜˜˜˜˜˜˜˜˜˜˜ ˜˜˜˜˜˜˜^˜
NormalizeProbes.c:471:77: warning: implicit conversion changes signedness: 'int' to 'size_t' (aka 'unsigned long') [-Wsign-conversion]
gsl_matrix_set(pairNumCount2,i,tempInt-1,gsl_matrix_get(pairNumCount2,i,tempInt-1)+1);
˜˜˜˜˜˜˜˜˜˜˜˜˜˜ ^
NormalizeProbes.c:471:86: warning: implicit conversion changes signedness: 'int' to 'size_t' (aka 'unsigned long') [-Wsign-conversion]
gsl_matrix_set(pairNumCount2,i,tempInt-1,gsl_matrix_get(pairNumCount2,i,tempInt-1)+1);
˜˜˜˜˜˜˜˜˜˜˜˜˜˜ ˜˜˜˜˜˜˜^˜
NormalizeProbes.c:473:36: warning: implicit conversion changes signedness: 'int' to 'size_t' (aka 'unsigned long') [-Wsign-conversion]
gsl_matrix_set(pairNumCount3,i,tempInt-1,gsl_matrix_get(pairNumCount3,i,tempInt-1)+1);
˜˜˜˜˜˜˜˜˜˜˜˜˜˜ ^
NormalizeProbes.c:473:45: warning: implicit conversion changes signedness: 'int' to 'size_t' (aka 'unsigned long') [-Wsign-conversion]
gsl_matrix_set(pairNumCount3,i,tempInt-1,gsl_matrix_get(pairNumCount3,i,tempInt-1)+1);
˜˜˜˜˜˜˜˜˜˜˜˜˜˜ ˜˜˜˜˜˜˜^˜
NormalizeProbes.c:473:77: warning: implicit conversion changes signedness: 'int' to 'size_t' (aka 'unsigned long') [-Wsign-conversion]
gsl_matrix_set(pairNumCount3,i,tempInt-1,gsl_matrix_get(pairNumCount3,i,tempInt-1)+1);
˜˜˜˜˜˜˜˜˜˜˜˜˜˜ ^
NormalizeProbes.c:473:86: warning: implicit conversion changes signedness: 'int' to 'size_t' (aka 'unsigned long') [-Wsign-conversion]
gsl_matrix_set(pairNumCount3,i,tempInt-1,gsl_matrix_get(pairNumCount3,i,tempInt-1)+1);
˜˜˜˜˜˜˜˜˜˜˜˜˜˜ ˜˜˜˜˜˜˜^˜
NormalizeProbes.c:475:36: warning: implicit conversion changes signedness: 'int' to 'size_t' (aka 'unsigned long') [-Wsign-conversion]
gsl_matrix_set(pairNumCount4,i,tempInt-1,gsl_matrix_get(pairNumCount4,i,tempInt-1)+1);
˜˜˜˜˜˜˜˜˜˜˜˜˜˜ ^
NormalizeProbes.c:475:45: warning: implicit conversion changes signedness: 'int' to 'size_t' (aka 'unsigned long') [-Wsign-conversion]
gsl_matrix_set(pairNumCount4,i,tempInt-1,gsl_matrix_get(pairNumCount4,i,tempInt-1)+1);
˜˜˜˜˜˜˜˜˜˜˜˜˜˜ ˜˜˜˜˜˜˜^˜
NormalizeProbes.c:475:77: warning: implicit conversion changes signedness: 'int' to 'size_t' (aka 'unsigned long') [-Wsign-conversion]
gsl_matrix_set(pairNumCount4,i,tempInt-1,gsl_matrix_get(pairNumCount4,i,tempInt-1)+1);
˜˜˜˜˜˜˜˜˜˜˜˜˜˜ ^
NormalizeProbes.c:475:86: warning: implicit conversion changes signedness: 'int' to 'size_t' (aka 'unsigned long') [-Wsign-conversion]
gsl_matrix_set(pairNumCount4,i,tempInt-1,gsl_matrix_get(pairNumCount4,i,tempInt-1)+1);
˜˜˜˜˜˜˜˜˜˜˜˜˜˜ ˜˜˜˜˜˜˜^˜
NormalizeProbes.c:459:30: warning: implicit conversion loses integer precision: 'size_t' (aka 'unsigned long') to 'int' [-Wshorten-64-to-32]
int nProbes=pairNumCount1->size1;
˜˜˜˜˜˜˜ ˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜^˜˜˜˜
NormalizeProbes.c:642:55: warning: implicit conversion changes signedness: 'int' to 'size_t' (aka 'unsigned long') [-Wsign-conversion]
vectorTmp=gsl_vector_view_array(dataInRegion, nProbesRegion);
˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜ ^˜˜˜˜˜˜˜˜˜˜˜˜
NormalizeProbes.c:644:41: warning: implicit conversion changes signedness: 'int' to 'size_t' (aka 'unsigned long') [-Wsign-conversion]
vectorInRegion=gsl_vector_alloc(nProbesRegion);
˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜ ^˜˜˜˜˜˜˜˜˜˜˜˜
NormalizeProbes.c:650:74: warning: implicit conversion changes signedness: 'int' to 'size_t' (aka 'unsigned long') [-Wsign-conversion]
cMin=gsl_stats_quantile_from_sorted_data(vectorInRegion->data,1, nProbesRegion, .1);
˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜ ^˜˜˜˜˜˜˜˜˜˜˜˜
NormalizeProbes.c:651:74: warning: implicit conversion changes signedness: 'int' to 'size_t' (aka 'unsigned long') [-Wsign-conversion]
cMax=gsl_stats_quantile_from_sorted_data(vectorInRegion->data,1, nProbesRegion, .9);
˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜ ^˜˜˜˜˜˜˜˜˜˜˜˜
NormalizeProbes.c:676:53: warning: implicit conversion changes signedness: 'int' to 'size_t' (aka 'unsigned long') [-Wsign-conversion]
vectorTmp=gsl_vector_view_array(dataInRegion, nProbesRegion);
˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜ ^˜˜˜˜˜˜˜˜˜˜˜˜
NormalizeProbes.c:678:39: warning: implicit conversion changes signedness: 'int' to 'size_t' (aka 'unsigned long') [-Wsign-conversion]
vectorInRegion=gsl_vector_alloc(nProbesRegion);
˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜ ^˜˜˜˜˜˜˜˜˜˜˜˜
NormalizeProbes.c:684:72: warning: implicit conversion changes signedness: 'int' to 'size_t' (aka 'unsigned long') [-Wsign-conversion]
cMin=gsl_stats_quantile_from_sorted_data(vectorInRegion->data,1, nProbesRegion, .1);
˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜ ^˜˜˜˜˜˜˜˜˜˜˜˜
NormalizeProbes.c:685:72: warning: implicit conversion changes signedness: 'int' to 'size_t' (aka 'unsigned long') [-Wsign-conversion]
cMax=gsl_stats_quantile_from_sorted_data(vectorInRegion->data,1, nProbesRegion, .9);
˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜ ^˜˜˜˜˜˜˜˜˜˜˜˜
NormalizeProbes.c:745:52: warning: implicit conversion changes signedness: 'int' to 'size_t' (aka 'unsigned long') [-Wsign-conversion]
gsl_vector *NoOverLapMATScores=gsl_vector_calloc(nRegionsMax);
˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜ ^˜˜˜˜˜˜˜˜˜˜
NormalizeProbes.c:756:39: warning: implicit conversion changes signedness: 'int' to 'size_t' (aka 'unsigned long') [-Wsign-conversion]
gsl_vector_set(NoOverLapMATScores,nRegions,MATScores[p1]);
˜˜˜˜˜˜˜˜˜˜˜˜˜˜ ^˜˜˜˜˜˜˜
NormalizeProbes.c:766:41: warning: implicit conversion changes signedness: 'int' to 'size_t' (aka 'unsigned long') [-Wsign-conversion]
gsl_sort(NoOverLapMATScores->data, 1, nRegions);
˜˜˜˜˜˜˜˜ ^˜˜˜˜˜˜˜
NormalizeProbes.c:767:71: warning: implicit conversion changes signedness: 'int' to 'size_t' (aka 'unsigned long') [-Wsign-conversion]
*mu0=gsl_stats_median_from_sorted_data(NoOverLapMATScores->data, 1, nRegions);
˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜ ^˜˜˜˜˜˜˜
NormalizeProbes.c:771:45: warning: implicit conversion changes signedness: 'int' to 'size_t' (aka 'unsigned long') [-Wsign-conversion]
NoOverLapMATScoresMinus=gsl_vector_calloc(nRegions);
˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜ ^˜˜˜˜˜˜˜
NormalizeProbes.c:775:44: warning: implicit conversion changes signedness: 'int' to 'size_t' (aka 'unsigned long') [-Wsign-conversion]
gsl_vector_set(NoOverLapMATScoresMinus,i,gsl_vector_get(NoOverLapMATScores,i));
˜˜˜˜˜˜˜˜˜˜˜˜˜˜ ^
NormalizeProbes.c:775:80: warning: implicit conversion changes signedness: 'int' to 'size_t' (aka 'unsigned long') [-Wsign-conversion]
gsl_vector_set(NoOverLapMATScoresMinus,i,gsl_vector_get(NoOverLapMATScores,i));
˜˜˜˜˜˜˜˜˜˜˜˜˜˜ ^
NormalizeProbes.c:779:44: warning: implicit conversion changes signedness: 'int' to 'size_t' (aka 'unsigned long') [-Wsign-conversion]
gsl_vector_set(NoOverLapMATScoresMinus,i,2**mu0-gsl_vector_get(NoOverLapMATScores,i-(int)nRegions/2));
˜˜˜˜˜˜˜˜˜˜˜˜˜˜ ^
NormalizeProbes.c:779:88: warning: implicit conversion changes signedness: 'int' to 'size_t' (aka 'unsigned long') [-Wsign-conversion]
gsl_vector_set(NoOverLapMATScoresMinus,i,2**mu0-gsl_vector_get(NoOverLapMATScores,i-(int)nRegions/2));
˜˜˜˜˜˜˜˜˜˜˜˜˜˜ ˜^˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜
NormalizeProbes.c:782:58: warning: implicit conversion changes signedness: 'int' to 'size_t' (aka 'unsigned long') [-Wsign-conversion]
*sigma0=gsl_stats_sd(NoOverLapMATScoresMinus->data, 1, nRegions);
˜˜˜˜˜˜˜˜˜˜˜˜ ^˜˜˜˜˜˜˜
NormalizeProbes.c:893:28: warning: implicit conversion changes signedness: 'int' to 'size_t' (aka 'unsigned long') [-Wsign-conversion]
weight=gsl_vector_calloc(*nProbes);
˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜ ^˜˜˜˜˜˜˜
NormalizeProbes.c:894:34: warning: implicit conversion changes signedness: 'int' to 'size_t' (aka 'unsigned long') [-Wsign-conversion]
fittedSorted=gsl_vector_calloc(nProbesTotal);
˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜ ^˜˜˜˜˜˜˜˜˜˜˜
NormalizeProbes.c:898:30: warning: implicit conversion changes signedness: 'int' to 'size_t' (aka 'unsigned long') [-Wsign-conversion]
sdBins=gsl_vector_calloc(nBins);
˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜ ^˜˜˜˜
NormalizeProbes.c:899:78: warning: implicit conversion changes signedness: 'int' to 'size_t' (aka 'unsigned long') [-Wsign-conversion]
yBin=gsl_vector_calloc(nProbesPerBin+nProbesTotal-nProbesPerBin*(nBins-1)+1);
˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜ ˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜^˜
NormalizeProbes.c:902:53: warning: implicit conversion changes signedness: 'int' to 'size_t' (aka 'unsigned long') [-Wsign-conversion]
copyNumberVector=gsl_vector_view_array(copyNumber,nProbesTotal);
˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜ ^˜˜˜˜˜˜˜˜˜˜˜
NormalizeProbes.c:903:24: warning: implicit conversion changes signedness: 'int' to 'size_t' (aka 'unsigned long') [-Wsign-conversion]
XR=gsl_vector_calloc(nVariables);
˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜ ^˜˜˜˜˜˜˜˜˜
NormalizeProbes.c:908:25: warning: implicit conversion changes signedness: 'int' to 'size_t' (aka 'unsigned long') [-Wsign-conversion]
X=gsl_matrix_calloc(*nProbes,nVariables);
˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜ ^˜˜˜˜˜˜˜
NormalizeProbes.c:908:34: warning: implicit conversion changes signedness: 'int' to 'size_t' (aka 'unsigned long') [-Wsign-conversion]
X=gsl_matrix_calloc(*nProbes,nVariables);
˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜ ^˜˜˜˜˜˜˜˜˜
NormalizeProbes.c:914:25: warning: implicit conversion changes signedness: 'int' to 'size_t' (aka 'unsigned long') [-Wsign-conversion]
X=gsl_matrix_calloc(*nProbes, nVariables);
˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜ ^˜˜˜˜˜˜˜
NormalizeProbes.c:914:35: warning: implicit conversion changes signedness: 'int' to 'size_t' (aka 'unsigned long') [-Wsign-conversion]
X=gsl_matrix_calloc(*nProbes, nVariables);
˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜ ^˜˜˜˜˜˜˜˜˜
NormalizeProbes.c:925:25: warning: implicit conversion changes signedness: 'int' to 'size_t' (aka 'unsigned long') [-Wsign-conversion]
beta=gsl_vector_alloc(nVariables);
˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜ ^˜˜˜˜˜˜˜˜˜
NormalizeProbes.c:926:28: warning: implicit conversion changes signedness: 'int' to 'size_t' (aka 'unsigned long') [-Wsign-conversion]
betaTmp=gsl_vector_alloc(nVariables);
˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜ ^˜˜˜˜˜˜˜˜˜
NormalizeProbes.c:927:23: warning: implicit conversion changes signedness: 'int' to 'size_t' (aka 'unsigned long') [-Wsign-conversion]
H=gsl_matrix_calloc(nVariables,nVariables);
˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜ ^˜˜˜˜˜˜˜˜˜
NormalizeProbes.c:927:34: warning: implicit conversion changes signedness: 'int' to 'size_t' (aka 'unsigned long') [-Wsign-conversion]
H=gsl_matrix_calloc(nVariables,nVariables);
˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜ ^˜˜˜˜˜˜˜˜˜
NormalizeProbes.c:928:38: warning: implicit conversion changes signedness: 'int' to 'size_t' (aka 'unsigned long') [-Wsign-conversion]
indexSorted=gsl_permutation_calloc(nProbesTotal);
˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜ ^˜˜˜˜˜˜˜˜˜˜˜
NormalizeProbes.c:940:51: warning: implicit conversion changes signedness: 'int' to 'size_t' (aka 'unsigned long') [-Wsign-conversion]
yVector=gsl_vector_view_array(y+j*nProbesTotal, *nProbes);
˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜ ^˜˜˜˜˜˜˜
NormalizeProbes.c:947:43: warning: implicit conversion changes signedness: 'int' to 'size_t' (aka 'unsigned long') [-Wsign-conversion]
meanY=gsl_stats_mean(y+j*nProbesTotal,1,*nProbes);
˜˜˜˜˜˜˜˜˜˜˜˜˜˜ ^˜˜˜˜˜˜˜
NormalizeProbes.c:953:29: warning: implicit conversion changes signedness: 'int' to 'size_t' (aka 'unsigned long') [-Wsign-conversion]
xRow=gsl_matrix_row(X,i);
˜˜˜˜˜˜˜˜˜˜˜˜˜˜ ^
NormalizeProbes.c:998:31: warning: implicit conversion changes signedness: 'int' to 'size_t' (aka 'unsigned long') [-Wsign-conversion]
gsl_vector_set(weight,i,(4.0+1.0)/(4.0+*nProbes/RSS*gsl_pow_2(y[j*nProbesTotal+i]-yNormalized[j*nProbesTotal+i])));
˜˜˜˜˜˜˜˜˜˜˜˜˜˜ ^
NormalizeProbes.c:1000:31: warning: implicit conversion changes signedness: 'int' to 'size_t' (aka 'unsigned long') [-Wsign-conversion]
xRow=gsl_matrix_row(X,i);
˜˜˜˜˜˜˜˜˜˜˜˜˜˜ ^
NormalizeProbes.c:1001:67: warning: implicit conversion changes signedness: 'int' to 'size_t' (aka 'unsigned long') [-Wsign-conversion]
gsl_vector_scale(&xRow.vector, sqrt(gsl_vector_get(weight,i)));
˜˜˜˜˜˜˜˜˜˜˜˜˜˜ ^
NormalizeProbes.c:1003:56: warning: implicit conversion changes signedness: 'int' to 'size_t' (aka 'unsigned long') [-Wsign-conversion]
y[j*nProbesTotal+i]=sqrt(gsl_vector_get(weight,i))*y[j*nProbesTotal+i];
˜˜˜˜˜˜˜˜˜˜˜˜˜˜ ^
NormalizeProbes.c:1019:33: warning: implicit conversion changes signedness: 'int' to 'size_t' (aka 'unsigned long') [-Wsign-conversion]
xRow=gsl_matrix_row(X,i);
˜˜˜˜˜˜˜˜˜˜˜˜˜˜ ^
NormalizeProbes.c:1023:78: warning: implicit conversion changes signedness: 'int' to 'size_t' (aka 'unsigned long') [-Wsign-conversion]
y[j*nProbesTotal+i]=y[j*nProbesTotal+i]/sqrt(gsl_vector_get(weight,i));
˜˜˜˜˜˜˜˜˜˜˜˜˜˜ ^
NormalizeProbes.c:1024:98: warning: implicit conversion changes signedness: 'int' to 'size_t' (aka 'unsigned long') [-Wsign-conversion]
yNormalized[j*nProbesTotal+i]=yNormalized[j*nProbesTotal+i]/sqrt(gsl_vector_get(weight,i));
˜˜˜˜˜˜˜˜˜˜˜˜˜˜ ^
NormalizeProbes.c:1028:72: warning: implicit conversion changes signedness: 'int' to 'size_t' (aka 'unsigned long') [-Wsign-conversion]
gsl_vector_scale(&xRow.vector, 1./sqrt(gsl_vector_get(weight,i)));
˜˜˜˜˜˜˜˜˜˜˜˜˜˜ ^
NormalizeProbes.c:1067:36: warning: implicit conversion changes signedness: 'int' to 'size_t' (aka 'unsigned long') [-Wsign-conversion]
gsl_vector_set(fittedSorted, i, yNormalized[j*nProbesTotal+i]);
˜˜˜˜˜˜˜˜˜˜˜˜˜˜ ^
NormalizeProbes.c:1074:29: warning: implicit conversion changes signedness: 'int' to 'size_t' (aka 'unsigned long') [-Wsign-conversion]
gsl_vector_set(yBin,k,y[j*nProbesTotal+indexSorted->data[nProbesPerBin*i+k]]);
˜˜˜˜˜˜˜˜˜˜˜˜˜˜ ^
NormalizeProbes.c:1074:34: warning: implicit conversion changes signedness: 'int' to 'unsigned long' [-Wsign-conversion]
gsl_vector_set(yBin,k,y[j*nProbesTotal+indexSorted->data[nProbesPerBin*i+k]]);
˜^˜˜˜˜˜˜˜˜˜˜˜˜˜
NormalizeProbes.c:1075:29: warning: implicit conversion changes signedness: 'int' to 'size_t' (aka 'unsigned long') [-Wsign-conversion]
gsl_vector_set(sdBins,i,gsl_stats_sd(yBin->data,1,nProbesPerBin));
˜˜˜˜˜˜˜˜˜˜˜˜˜˜ ^
NormalizeProbes.c:1075:57: warning: implicit conversion changes signedness: 'int' to 'size_t' (aka 'unsigned long') [-Wsign-conversion]
gsl_vector_set(sdBins,i,gsl_stats_sd(yBin->data,1,nProbesPerBin));
˜˜˜˜˜˜˜˜˜˜˜˜ ^˜˜˜˜˜˜˜˜˜˜˜˜
NormalizeProbes.c:1078:22: warning: implicit conversion changes signedness: 'int' to 'unsigned long' [-Wsign-conversion]
yNormalized[j*nProbesTotal+indexSorted->data[nProbesPerBin*i+k]]=(y[j*nProbesTotal+indexSorted->data[nProbesPerBin*i+k]]-yNormalized[j*nProbesTotal+indexSorted->data[nProbesPerBin*i+k]])/gsl_vector_get(sdBins,i);
˜^˜˜˜˜˜˜˜˜˜˜˜˜˜
NormalizeProbes.c:1078:78: warning: implicit conversion changes signedness: 'int' to 'unsigned long' [-Wsign-conversion]
yNormalized[j*nProbesTotal+indexSorted->data[nProbesPerBin*i+k]]=(y[j*nProbesTotal+indexSorted->data[nProbesPerBin*i+k]]-yNormalized[j*nProbesTotal+indexSorted->data[nProbesPerBin*i+k]])/gsl_vector_get(sdBins,i);
˜^˜˜˜˜˜˜˜˜˜˜˜˜˜
NormalizeProbes.c:1078:143: warning: implicit conversion changes signedness: 'int' to 'unsigned long' [-Wsign-conversion]
yNormalized[j*nProbesTotal+indexSorted->data[nProbesPerBin*i+k]]=(y[j*nProbesTotal+indexSorted->data[nProbesPerBin*i+k]]-yNormalized[j*nProbesTotal+indexSorted->data[nProbesPerBin*i+k]])/gsl_vector_get(sdBins,i);
˜^˜˜˜˜˜˜˜˜˜˜˜˜˜
NormalizeProbes.c:1078:218: warning: implicit conversion changes signedness: 'int' to 'size_t' (aka 'unsigned long') [-Wsign-conversion]
yNormalized[j*nProbesTotal+indexSorted->data[nProbesPerBin*i+k]]=(y[j*nProbesTotal+indexSorted->data[nProbesPerBin*i+k]]-yNormalized[j*nProbesTotal+indexSorted->data[nProbesPerBin*i+k]])/gsl_vector_get(sdBins,i);
˜˜˜˜˜˜˜˜˜˜˜˜˜˜ ^
NormalizeProbes.c:1082:27: warning: implicit conversion changes signedness: 'int' to 'size_t' (aka 'unsigned long') [-Wsign-conversion]
gsl_vector_set(yBin,k,y[j*nProbesTotal+indexSorted->data[nProbesPerBin*(nBins-1)+k]]);
˜˜˜˜˜˜˜˜˜˜˜˜˜˜ ^
NormalizeProbes.c:1082:32: warning: implicit conversion changes signedness: 'int' to 'unsigned long' [-Wsign-conversion]
gsl_vector_set(yBin,k,y[j*nProbesTotal+indexSorted->data[nProbesPerBin*(nBins-1)+k]]);
˜^˜˜˜˜˜˜˜˜˜˜˜˜˜
NormalizeProbes.c:1083:32: warning: implicit conversion changes signedness: 'int' to 'size_t' (aka 'unsigned long') [-Wsign-conversion]
gsl_vector_set(sdBins,nBins-1,gsl_stats_sd(yBin->data,1,nProbesTotal-nProbesPerBin*(nBins-1)));
˜˜˜˜˜˜˜˜˜˜˜˜˜˜ ˜˜˜˜˜^˜
NormalizeProbes.c:1083:73: warning: implicit conversion changes signedness: 'int' to 'size_t' (aka 'unsigned long') [-Wsign-conversion]
gsl_vector_set(sdBins,nBins-1,gsl_stats_sd(yBin->data,1,nProbesTotal-nProbesPerBin*(nBins-1)));
˜˜˜˜˜˜˜˜˜˜˜˜ ˜˜˜˜˜˜˜˜˜˜˜˜^˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜
NormalizeProbes.c:1085:20: warning: implicit conversion changes signedness: 'int' to 'unsigned long' [-Wsign-conversion]
yNormalized[j*nProbesTotal+indexSorted->data[nProbesPerBin*(nBins-1)+k]]=(y[j*nProbesTotal+indexSorted->data[nProbesPerBin*(nBins-1)+k]]-yNormalized[j*nProbesTotal+indexSorted->data[nProbesPerBin*(nBins-1)+k]])/gsl_vector_get(sdBins,nBins-1);
˜^˜˜˜˜˜˜˜˜˜˜˜˜˜
NormalizeProbes.c:1085:84: warning: implicit conversion changes signedness: 'int' to 'unsigned long' [-Wsign-conversion]
yNormalized[j*nProbesTotal+indexSorted->data[nProbesPerBin*(nBins-1)+k]]=(y[j*nProbesTotal+indexSorted->data[nProbesPerBin*(nBins-1)+k]]-yNormalized[j*nProbesTotal+indexSorted->data[nProbesPerBin*(nBins-1)+k]])/gsl_vector_get(sdBins,nBins-1);
˜^˜˜˜˜˜˜˜˜˜˜˜˜˜
NormalizeProbes.c:1085:157: warning: implicit conversion changes signedness: 'int' to 'unsigned long' [-Wsign-conversion]
yNormalized[j*nProbesTotal+indexSorted->data[nProbesPerBin*(nBins-1)+k]]=(y[j*nProbesTotal+indexSorted->data[nProbesPerBin*(nBins-1)+k]]-yNormalized[j*nProbesTotal+indexSorted->data[nProbesPerBin*(nBins-1)+k]])/gsl_vector_get(sdBins,nBins-1);
˜^˜˜˜˜˜˜˜˜˜˜˜˜˜
NormalizeProbes.c:1085:245: warning: implicit conversion changes signedness: 'int' to 'size_t' (aka 'unsigned long') [-Wsign-conversion]
yNormalized[j*nProbesTotal+indexSorted->data[nProbesPerBin*(nBins-1)+k]]=(y[j*nProbesTotal+indexSorted->data[nProbesPerBin*(nBins-1)+k]]-yNormalized[j*nProbesTotal+indexSorted->data[nProbesPerBin*(nBins-1)+k]])/gsl_vector_get(sdBins,nBins-1);
˜˜˜˜˜˜˜˜˜˜˜˜˜˜ ˜˜˜˜˜^˜
NormalizeProbes.c:1109:18: warning: equality comparison with extraneous parentheses [-Wparentheses-equality]
if((*MATScaling==1))
˜˜˜˜˜˜˜˜˜˜˜^˜˜
NormalizeProbes.c:1109:18: note: remove extraneous parentheses around the comparison to silence this warning
if((*MATScaling==1))
˜ ^ ˜
NormalizeProbes.c:1109:18: note: use '=' to turn this equality comparison into an assignment
if((*MATScaling==1))
^˜
=
188 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 rMAT.so BARFileData.o BARFileWriter.o BARReader.o BARWriter.o BPMAPFileData.o BPMAPfunctions.o DeclareAll.o FileIO.o FileWriter.o NormalizeProbes.o -L/usr/local/lib -lgsl -lgslcblas -lm -F/Library/Frameworks/R.framework/.. -framework R -Wl,-framework -Wl,CoreFoundation
installing to /Users/biocbuild/bbs-2.12-bioc/meat/rMAT.buildbin-libdir/rMAT/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 (rMAT)
>>>>>>>
>>>>>>> FIXING LINKS FOR rMAT.buildbin-libdir/rMAT/libs//rMAT.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" "rMAT.buildbin-libdir/rMAT/libs//rMAT.so"
install_name_tool -change "/usr/local/lib/libgfortran.2.dylib" "/Library/Frameworks/R.framework/Versions/3.0/Resources/lib/libgfortran.2.dylib" "rMAT.buildbin-libdir/rMAT/libs//rMAT.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" "rMAT.buildbin-libdir/rMAT/libs//rMAT.so"
install_name_tool -change "/usr/local/lib/libreadline.dylib" "/Library/Frameworks/R.framework/Versions/3.0/Resources/lib/libreadline.dylib" "rMAT.buildbin-libdir/rMAT/libs//rMAT.so"