>>>>>>>
>>>>>>> INSTALLATION WITH 'R CMD INSTALL --preclean --no-multiarch --library=BitSeq.buildbin-libdir BitSeq_1.4.2.tar.gz'
>>>>>>>
* installing *source* package 'BitSeq' ...
configure: Version def: -DBS_VERSION=\"1.4.2\"
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 support OpenMP... unsupported
configure: No Open MP support.
configure: SAM_INCLUDE: /Library/Frameworks/R.framework/Versions/3.0/Resources/library/Rsamtools/usretc//Rsamtools.mk
configure: creating ./config.status
config.status: creating src/Makevars
config.status: creating src/Makevars.win
** libs
clang++ -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -DPACKAGE_NAME=\"Bitseq\" -DPACKAGE_TARNAME=\"bitseq\" -DPACKAGE_VERSION=\"1.4.x\" -DPACKAGE_STRING=\"Bitseq\ 1.4.x\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DBS_VERSION=\"1.4.2\" -DBIOC_BUILD=1 -D_USE_KNETFILE -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -I/usr/local/include -I"/Library/Frameworks/R.framework/Versions/3.0/Resources/library/Rsamtools/include" -I"/Library/Frameworks/R.framework/Versions/3.0/Resources/library/zlibbioc/include" -I. -fPIC -mtune=native -g -O2 -Wall -pedantic -Wconversion -c ArgumentParser.cpp -o ArgumentParser.o
In file included from ArgumentParser.cpp:6:
./common.h:17:17: warning: variadic macros are a C99 feature [-Wvariadic-macros]
#define message(...) Rprintf(__VA_ARGS__)
^
ArgumentParser.cpp:14:21: warning: implicit conversion changes signedness: 'size_type' (aka 'unsigned long') to 'long' [-Wsign-conversion]
long pos=0,f=0,n=input.size();
˜ ^˜˜˜˜˜˜˜˜˜˜˜
ArgumentParser.cpp:16:9: warning: implicit conversion changes signedness: 'size_type' (aka 'unsigned long') to 'long' [-Wsign-conversion]
f=input.find(space,pos);
˜^˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜
ArgumentParser.cpp:16:26: warning: implicit conversion changes signedness: 'long' to 'size_type' (aka 'unsigned long') [-Wsign-conversion]
f=input.find(space,pos);
˜˜˜˜˜ ^˜˜
ArgumentParser.cpp:20:45: warning: implicit conversion changes signedness: 'long' to 'size_type' (aka 'unsigned long') [-Wsign-conversion]
ret.push_back(atof(input.substr(pos,f-pos).c_str()));
˜˜˜˜˜ ^˜˜
ArgumentParser.cpp:20:50: warning: implicit conversion changes signedness: 'long' to 'size_type' (aka 'unsigned long') [-Wsign-conversion]
ret.push_back(atof(input.substr(pos,f-pos).c_str()));
˜˜˜˜˜ ˜^˜˜˜
ArgumentParser.cpp:25:45: warning: implicit conversion changes signedness: 'long' to 'size_type' (aka 'unsigned long') [-Wsign-conversion]
if(pos<n)ret.push_back(atof(input.substr(pos,n-pos).c_str()));
˜˜˜˜˜ ^˜˜
ArgumentParser.cpp:25:50: warning: implicit conversion changes signedness: 'long' to 'size_type' (aka 'unsigned long') [-Wsign-conversion]
if(pos<n)ret.push_back(atof(input.substr(pos,n-pos).c_str()));
˜˜˜˜˜ ˜^˜˜˜
ArgumentParser.cpp:124:29: warning: implicit conversion changes signedness: 'long' to 'size_type' (aka 'unsigned long') [-Wsign-conversion]
if(! isSet(compulsory[i])){
˜˜˜˜˜˜˜˜˜˜ ^
ArgumentParser.cpp:125:54: warning: implicit conversion changes signedness: 'long' to 'size_type' (aka 'unsigned long') [-Wsign-conversion]
error("Missing option \"%s\"\n",(compulsory[i]).c_str());
˜˜˜˜˜˜˜˜˜˜ ^
ArgumentParser.cpp:137:32: warning: implicit conversion changes signedness: 'long' to 'size_type' (aka 'unsigned long') [-Wsign-conversion]
message("%s ",(arguments[i]).c_str());
˜˜˜˜˜˜˜˜˜ ^
./common.h:17:30: note: expanded from macro 'message'
#define message(...) Rprintf(__VA_ARGS__)
^
11 warnings generated.
clang++ -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -DPACKAGE_NAME=\"Bitseq\" -DPACKAGE_TARNAME=\"bitseq\" -DPACKAGE_VERSION=\"1.4.x\" -DPACKAGE_STRING=\"Bitseq\ 1.4.x\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DBS_VERSION=\"1.4.2\" -DBIOC_BUILD=1 -D_USE_KNETFILE -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -I/usr/local/include -I"/Library/Frameworks/R.framework/Versions/3.0/Resources/library/Rsamtools/include" -I"/Library/Frameworks/R.framework/Versions/3.0/Resources/library/zlibbioc/include" -I. -fPIC -mtune=native -g -O2 -Wall -pedantic -Wconversion -c CollapsedSampler.cpp -o CollapsedSampler.o
In file included from CollapsedSampler.cpp:5:
In file included from ./CollapsedSampler.h:3:
In file included from ./Sampler.h:6:
In file included from ./boost/random/mersenne_twister.hpp:29:
In file included from ./boost/random/detail/seed_impl.hpp:27:
In file included from ./boost/random/detail/const_mod.hpp:23:
./boost/random/detail/large_arithmetic.hpp:94:14: warning: implicit conversion changes signedness: 'int' to 'unsigned int' [-Wsign-conversion]
q -= error;
˜˜ ^˜˜˜˜
./boost/random/detail/large_arithmetic.hpp:95:21: warning: implicit conversion changes signedness: 'int' to 'unsigned long' [-Wsign-conversion]
rem = rem + error * m - diff;
^˜˜˜˜ ˜
In file included from CollapsedSampler.cpp:5:
In file included from ./CollapsedSampler.h:3:
In file included from ./Sampler.h:6:
./boost/random/mersenne_twister.hpp:493:14: warning: 'long long' is a C++11 extension [-Wc++11-long-long]
UINT64_C(0xb5026f5aa96619e9),29,UINT64_C(0x5555555555555555),17,
^
/usr/include/stdint.h:248:23: note: expanded from macro 'UINT64_C'
#define UINT64_C(v) (v ## ULL)
^
<scratch space>:92:1: note: expanded from macro '0xb5026f5aa96619e9'
0xb5026f5aa96619e9ULL
^
In file included from CollapsedSampler.cpp:5:
In file included from ./CollapsedSampler.h:3:
In file included from ./Sampler.h:6:
./boost/random/mersenne_twister.hpp:493:46: warning: 'long long' is a C++11 extension [-Wc++11-long-long]
UINT64_C(0xb5026f5aa96619e9),29,UINT64_C(0x5555555555555555),17,
^
/usr/include/stdint.h:248:23: note: expanded from macro 'UINT64_C'
#define UINT64_C(v) (v ## ULL)
^
<scratch space>:92:1: note: expanded from macro '0x5555555555555555'
0x5555555555555555ULL
^
In file included from CollapsedSampler.cpp:5:
In file included from ./CollapsedSampler.h:3:
In file included from ./Sampler.h:6:
./boost/random/mersenne_twister.hpp:494:14: warning: 'long long' is a C++11 extension [-Wc++11-long-long]
UINT64_C(0x71d67fffeda60000),37,UINT64_C(0xfff7eee000000000),43,
^
/usr/include/stdint.h:248:23: note: expanded from macro 'UINT64_C'
#define UINT64_C(v) (v ## ULL)
^
<scratch space>:92:1: note: expanded from macro '0x71d67fffeda60000'
0x71d67fffeda60000ULL
^
In file included from CollapsedSampler.cpp:5:
In file included from ./CollapsedSampler.h:3:
In file included from ./Sampler.h:6:
./boost/random/mersenne_twister.hpp:494:46: warning: 'long long' is a C++11 extension [-Wc++11-long-long]
UINT64_C(0x71d67fffeda60000),37,UINT64_C(0xfff7eee000000000),43,
^
/usr/include/stdint.h:248:23: note: expanded from macro 'UINT64_C'
#define UINT64_C(v) (v ## ULL)
^
<scratch space>:92:1: note: expanded from macro '0xfff7eee000000000'
0xfff7eee000000000ULL
^
In file included from CollapsedSampler.cpp:5:
In file included from ./CollapsedSampler.h:3:
In file included from ./Sampler.h:6:
./boost/random/mersenne_twister.hpp:495:14: warning: 'long long' is a C++11 extension [-Wc++11-long-long]
UINT64_C(6364136223846793005)> mt19937_64;
^
/usr/include/stdint.h:248:23: note: expanded from macro 'UINT64_C'
#define UINT64_C(v) (v ## ULL)
^
<scratch space>:92:1: note: expanded from macro '6364136223846793005'
6364136223846793005ULL
^
In file included from CollapsedSampler.cpp:6:
./common.h:17:17: warning: variadic macros are a C99 feature [-Wvariadic-macros]
#define message(...) Rprintf(__VA_ARGS__)
^
CollapsedSampler.cpp:12:16: warning: implicit conversion changes signedness: 'long' to 'size_type' (aka 'unsigned long') [-Wsign-conversion]
Z.assign(Nmap,0);
˜ ^˜˜˜
CollapsedSampler.cpp:17:12: warning: implicit conversion changes signedness: 'int_least32_t' (aka 'int') to 'size_type' (aka 'unsigned long') [-Wsign-conversion]
Z[i]=k;
˜ ^
CollapsedSampler.cpp:18:12: warning: implicit conversion changes signedness: 'int_least32_t' (aka 'int') to 'size_type' (aka 'unsigned long') [-Wsign-conversion]
C[k]++;
˜ ^
CollapsedSampler.cpp:28:23: warning: implicit conversion changes signedness: 'long' to 'size_type' (aka 'unsigned long') [-Wsign-conversion]
vector<double> phi(m,0);
˜˜˜ ^
CollapsedSampler.cpp:40:9: warning: implicit conversion changes signedness: 'int' to 'size_type' (aka 'unsigned long') [-Wsign-conversion]
C[Z[i]]--; // use counts without the current one
˜ ^˜˜˜
CollapsedSampler.cpp:40:11: warning: implicit conversion changes signedness: 'int_least32_t' (aka 'int') to 'size_type' (aka 'unsigned long') [-Wsign-conversion]
C[Z[i]]--; // use counts without the current one
˜ ^
CollapsedSampler.cpp:45:17: warning: implicit conversion changes signedness: 'int_least32_t' (aka 'int') to 'size_type' (aka 'unsigned long') [-Wsign-conversion]
phi[j] = alignments->getProb(k) *
˜˜˜ ^
CollapsedSampler.cpp:49:17: warning: implicit conversion changes signedness: 'int_least32_t' (aka 'int') to 'size_type' (aka 'unsigned long') [-Wsign-conversion]
phi[j] = alignments->getProb(k) *
˜˜˜ ^
CollapsedSampler.cpp:51:33: warning: implicit conversion changes signedness: 'int_least32_t' (aka 'int') to 'size_type' (aka 'unsigned long') [-Wsign-conversion]
(dir->alpha + C[ alignments->getTrId(k) ]);
˜ ^˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜
CollapsedSampler.cpp:58:26: warning: implicit conversion changes signedness: 'int_least32_t' (aka 'int') to 'size_type' (aka 'unsigned long') [-Wsign-conversion]
probNorm += phi[j];
˜˜˜ ^
CollapsedSampler.cpp:64:21: warning: implicit conversion changes signedness: 'int_least32_t' (aka 'int') to 'size_type' (aka 'unsigned long') [-Wsign-conversion]
sum += phi[j];
˜˜˜ ^
CollapsedSampler.cpp:69:12: warning: implicit conversion changes signedness: 'int_least32_t' (aka 'int') to 'size_type' (aka 'unsigned long') [-Wsign-conversion]
Z[i] = 0;
˜ ^
CollapsedSampler.cpp:71:12: warning: implicit conversion changes signedness: 'int_least32_t' (aka 'int') to 'size_type' (aka 'unsigned long') [-Wsign-conversion]
Z[i] = alignments->getTrId(alignments->getReadsI(i) + j -1);
˜ ^
CollapsedSampler.cpp:73:10: warning: implicit conversion changes signedness: 'int' to 'size_type' (aka 'unsigned long') [-Wsign-conversion]
C[ Z[i] ]++;
˜ ^˜˜˜
CollapsedSampler.cpp:73:12: warning: implicit conversion changes signedness: 'int_least32_t' (aka 'int') to 'size_type' (aka 'unsigned long') [-Wsign-conversion]
C[ Z[i] ]++;
˜ ^
23 warnings generated.
clang++ -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -DPACKAGE_NAME=\"Bitseq\" -DPACKAGE_TARNAME=\"bitseq\" -DPACKAGE_VERSION=\"1.4.x\" -DPACKAGE_STRING=\"Bitseq\ 1.4.x\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DBS_VERSION=\"1.4.2\" -DBIOC_BUILD=1 -D_USE_KNETFILE -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -I/usr/local/include -I"/Library/Frameworks/R.framework/Versions/3.0/Resources/library/Rsamtools/include" -I"/Library/Frameworks/R.framework/Versions/3.0/Resources/library/zlibbioc/include" -I. -fPIC -mtune=native -g -O2 -Wall -pedantic -Wconversion -c FileHeader.cpp -o FileHeader.o
In file included from FileHeader.cpp:4:
./common.h:17:17: warning: variadic macros are a C99 feature [-Wvariadic-macros]
#define message(...) Rprintf(__VA_ARGS__)
^
FileHeader.cpp:19:21: warning: implicit conversion changes signedness: 'size_type' (aka 'unsigned long') to 'long' [-Wsign-conversion]
long pos=0,f=0,n=input.size();
˜ ^˜˜˜˜˜˜˜˜˜˜˜
FileHeader.cpp:21:9: warning: implicit conversion changes signedness: 'size_type' (aka 'unsigned long') to 'long' [-Wsign-conversion]
f=input.find(space,pos);
˜^˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜
FileHeader.cpp:21:26: warning: implicit conversion changes signedness: 'long' to 'size_type' (aka 'unsigned long') [-Wsign-conversion]
f=input.find(space,pos);
˜˜˜˜˜ ^˜˜
FileHeader.cpp:25:40: warning: implicit conversion changes signedness: 'long' to 'size_type' (aka 'unsigned long') [-Wsign-conversion]
ret.push_back(input.substr(pos,f-pos));
˜˜˜˜˜ ^˜˜
FileHeader.cpp:25:45: warning: implicit conversion changes signedness: 'long' to 'size_type' (aka 'unsigned long') [-Wsign-conversion]
ret.push_back(input.substr(pos,f-pos));
˜˜˜˜˜ ˜^˜˜˜
FileHeader.cpp:30:40: warning: implicit conversion changes signedness: 'long' to 'size_type' (aka 'unsigned long') [-Wsign-conversion]
if(pos<n)ret.push_back(input.substr(pos,n-pos));
˜˜˜˜˜ ^˜˜
FileHeader.cpp:30:45: warning: implicit conversion changes signedness: 'long' to 'size_type' (aka 'unsigned long') [-Wsign-conversion]
if(pos<n)ret.push_back(input.substr(pos,n-pos));
˜˜˜˜˜ ˜^˜˜˜
FileHeader.cpp:56:32: warning: implicit conversion changes signedness: 'long' to 'size_type' (aka 'unsigned long') [-Wsign-conversion]
if(values.count(words[i])==0)
˜˜˜˜˜ ^
FileHeader.cpp:57:26: warning: implicit conversion changes signedness: 'long' to 'size_type' (aka 'unsigned long') [-Wsign-conversion]
values[words[i]] = no_value;
˜˜˜˜˜ ^
FileHeader.cpp:60:35: warning: implicit conversion changes signedness: 'long' to 'size_type' (aka 'unsigned long') [-Wsign-conversion]
value = strtol(words[i+1].c_str(), &chP, 10);
˜˜˜˜˜ ˜^˜
FileHeader.cpp:64:29: warning: implicit conversion changes signedness: 'long' to 'size_type' (aka 'unsigned long') [-Wsign-conversion]
values[words[i]] = value;
˜˜˜˜˜ ^
12 warnings generated.
clang++ -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -DPACKAGE_NAME=\"Bitseq\" -DPACKAGE_TARNAME=\"bitseq\" -DPACKAGE_VERSION=\"1.4.x\" -DPACKAGE_STRING=\"Bitseq\ 1.4.x\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DBS_VERSION=\"1.4.2\" -DBIOC_BUILD=1 -D_USE_KNETFILE -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -I/usr/local/include -I"/Library/Frameworks/R.framework/Versions/3.0/Resources/library/Rsamtools/include" -I"/Library/Frameworks/R.framework/Versions/3.0/Resources/library/zlibbioc/include" -I. -fPIC -mtune=native -g -O2 -Wall -pedantic -Wconversion -c GibbsParameters.cpp -o GibbsParameters.o
In file included from GibbsParameters.cpp:6:
./common.h:17:17: warning: variadic macros are a C99 feature [-Wvariadic-macros]
#define message(...) Rprintf(__VA_ARGS__)
^
1 warning generated.
clang++ -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -DPACKAGE_NAME=\"Bitseq\" -DPACKAGE_TARNAME=\"bitseq\" -DPACKAGE_VERSION=\"1.4.x\" -DPACKAGE_STRING=\"Bitseq\ 1.4.x\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DBS_VERSION=\"1.4.2\" -DBIOC_BUILD=1 -D_USE_KNETFILE -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -I/usr/local/include -I"/Library/Frameworks/R.framework/Versions/3.0/Resources/library/Rsamtools/include" -I"/Library/Frameworks/R.framework/Versions/3.0/Resources/library/zlibbioc/include" -I. -fPIC -mtune=native -g -O2 -Wall -pedantic -Wconversion -c GibbsSampler.cpp -o GibbsSampler.o
In file included from GibbsSampler.cpp:5:
In file included from ./GibbsSampler.h:2:
In file included from ./Sampler.h:6:
In file included from ./boost/random/mersenne_twister.hpp:29:
In file included from ./boost/random/detail/seed_impl.hpp:27:
In file included from ./boost/random/detail/const_mod.hpp:23:
./boost/random/detail/large_arithmetic.hpp:94:14: warning: implicit conversion changes signedness: 'int' to 'unsigned int' [-Wsign-conversion]
q -= error;
˜˜ ^˜˜˜˜
./boost/random/detail/large_arithmetic.hpp:95:21: warning: implicit conversion changes signedness: 'int' to 'unsigned long' [-Wsign-conversion]
rem = rem + error * m - diff;
^˜˜˜˜ ˜
In file included from GibbsSampler.cpp:5:
In file included from ./GibbsSampler.h:2:
In file included from ./Sampler.h:6:
./boost/random/mersenne_twister.hpp:493:14: warning: 'long long' is a C++11 extension [-Wc++11-long-long]
UINT64_C(0xb5026f5aa96619e9),29,UINT64_C(0x5555555555555555),17,
^
/usr/include/stdint.h:248:23: note: expanded from macro 'UINT64_C'
#define UINT64_C(v) (v ## ULL)
^
<scratch space>:92:1: note: expanded from macro '0xb5026f5aa96619e9'
0xb5026f5aa96619e9ULL
^
In file included from GibbsSampler.cpp:5:
In file included from ./GibbsSampler.h:2:
In file included from ./Sampler.h:6:
./boost/random/mersenne_twister.hpp:493:46: warning: 'long long' is a C++11 extension [-Wc++11-long-long]
UINT64_C(0xb5026f5aa96619e9),29,UINT64_C(0x5555555555555555),17,
^
/usr/include/stdint.h:248:23: note: expanded from macro 'UINT64_C'
#define UINT64_C(v) (v ## ULL)
^
<scratch space>:92:1: note: expanded from macro '0x5555555555555555'
0x5555555555555555ULL
^
In file included from GibbsSampler.cpp:5:
In file included from ./GibbsSampler.h:2:
In file included from ./Sampler.h:6:
./boost/random/mersenne_twister.hpp:494:14: warning: 'long long' is a C++11 extension [-Wc++11-long-long]
UINT64_C(0x71d67fffeda60000),37,UINT64_C(0xfff7eee000000000),43,
^
/usr/include/stdint.h:248:23: note: expanded from macro 'UINT64_C'
#define UINT64_C(v) (v ## ULL)
^
<scratch space>:92:1: note: expanded from macro '0x71d67fffeda60000'
0x71d67fffeda60000ULL
^
In file included from GibbsSampler.cpp:5:
In file included from ./GibbsSampler.h:2:
In file included from ./Sampler.h:6:
./boost/random/mersenne_twister.hpp:494:46: warning: 'long long' is a C++11 extension [-Wc++11-long-long]
UINT64_C(0x71d67fffeda60000),37,UINT64_C(0xfff7eee000000000),43,
^
/usr/include/stdint.h:248:23: note: expanded from macro 'UINT64_C'
#define UINT64_C(v) (v ## ULL)
^
<scratch space>:92:1: note: expanded from macro '0xfff7eee000000000'
0xfff7eee000000000ULL
^
In file included from GibbsSampler.cpp:5:
In file included from ./GibbsSampler.h:2:
In file included from ./Sampler.h:6:
./boost/random/mersenne_twister.hpp:495:14: warning: 'long long' is a C++11 extension [-Wc++11-long-long]
UINT64_C(6364136223846793005)> mt19937_64;
^
/usr/include/stdint.h:248:23: note: expanded from macro 'UINT64_C'
#define UINT64_C(v) (v ## ULL)
^
<scratch space>:92:1: note: expanded from macro '6364136223846793005'
6364136223846793005ULL
^
In file included from GibbsSampler.cpp:6:
./common.h:17:17: warning: variadic macros are a C99 feature [-Wvariadic-macros]
#define message(...) Rprintf(__VA_ARGS__)
^
GibbsSampler.cpp:20:23: warning: implicit conversion changes signedness: 'long' to 'size_type' (aka 'unsigned long') [-Wsign-conversion]
vector<double> phi(m,0);
˜˜˜ ^
GibbsSampler.cpp:34:17: warning: implicit conversion changes signedness: 'long' to 'size_type' (aka 'unsigned long') [-Wsign-conversion]
phi[j] = alignments->getProb(k) * (1 - thetaAct);
˜˜˜ ^
GibbsSampler.cpp:36:17: warning: implicit conversion changes signedness: 'long' to 'size_type' (aka 'unsigned long') [-Wsign-conversion]
phi[j] = alignments->getProb(k) *
˜˜˜ ^
GibbsSampler.cpp:37:33: warning: implicit conversion changes signedness: 'int_least32_t' (aka 'int') to 'size_type' (aka 'unsigned long') [-Wsign-conversion]
thetaAct * theta[alignments->getTrId(k)];
˜˜˜˜˜ ^˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜
GibbsSampler.cpp:39:26: warning: implicit conversion changes signedness: 'long' to 'size_type' (aka 'unsigned long') [-Wsign-conversion]
probNorm += phi[j];
˜˜˜ ^
GibbsSampler.cpp:45:21: warning: implicit conversion changes signedness: 'long' to 'size_type' (aka 'unsigned long') [-Wsign-conversion]
sum += phi[j];
˜˜˜ ^
GibbsSampler.cpp:53:13: warning: implicit conversion changes signedness: 'int_least32_t' (aka 'int') to 'size_type' (aka 'unsigned long') [-Wsign-conversion]
C[ alignments->getTrId( alignments->getReadsI(i)+j-1 ) ]++;
˜ ^˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜
15 warnings generated.
clang++ -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -DPACKAGE_NAME=\"Bitseq\" -DPACKAGE_TARNAME=\"bitseq\" -DPACKAGE_VERSION=\"1.4.x\" -DPACKAGE_STRING=\"Bitseq\ 1.4.x\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DBS_VERSION=\"1.4.2\" -DBIOC_BUILD=1 -D_USE_KNETFILE -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -I/usr/local/include -I"/Library/Frameworks/R.framework/Versions/3.0/Resources/library/Rsamtools/include" -I"/Library/Frameworks/R.framework/Versions/3.0/Resources/library/zlibbioc/include" -I. -fPIC -mtune=native -g -O2 -Wall -pedantic -Wconversion -c PosteriorSamples.cpp -o PosteriorSamples.o
In file included from PosteriorSamples.cpp:9:
./common.h:17:17: warning: variadic macros are a C99 feature [-Wvariadic-macros]
#define message(...) Rprintf(__VA_ARGS__)
^
PosteriorSamples.cpp:20:15: warning: implicit conversion changes signedness: 'long' to 'size_type' (aka 'unsigned long') [-Wsign-conversion]
if((str[i]>='A')&&(str[i]<='Z'))str[i]-='A'-'a';
˜˜˜ ^
PosteriorSamples.cpp:20:30: warning: implicit conversion changes signedness: 'long' to 'size_type' (aka 'unsigned long') [-Wsign-conversion]
if((str[i]>='A')&&(str[i]<='Z'))str[i]-='A'-'a';
˜˜˜ ^
PosteriorSamples.cpp:20:43: warning: implicit conversion changes signedness: 'long' to 'size_type' (aka 'unsigned long') [-Wsign-conversion]
if((str[i]>='A')&&(str[i]<='Z'))str[i]-='A'-'a';
˜˜˜ ^
PosteriorSamples.cpp:59:26: warning: implicit conversion changes signedness: 'long' to 'size_type' (aka 'unsigned long') [-Wsign-conversion]
lines=vector<long>(M,-1);
˜˜˜˜˜˜ ^
PosteriorSamples.cpp:67:22: warning: implicit conversion changes signedness: 'long' to 'size_type' (aka 'unsigned long') [-Wsign-conversion]
samples.resize(M,vector<double>(N,0));
˜˜˜˜˜˜˜ ^
PosteriorSamples.cpp:67:39: warning: implicit conversion changes signedness: 'long' to 'size_type' (aka 'unsigned long') [-Wsign-conversion]
samples.resize(M,vector<double>(N,0));
˜˜˜˜˜˜ ^
PosteriorSamples.cpp:70:31: warning: implicit conversion changes signedness: 'long' to 'size_type' (aka 'unsigned long') [-Wsign-conversion]
samplesF>>samples[j][i];
˜˜˜˜˜˜˜ ^
PosteriorSamples.cpp:70:34: warning: implicit conversion changes signedness: 'long' to 'size_type' (aka 'unsigned long') [-Wsign-conversion]
samplesF>>samples[j][i];
˜˜˜˜˜˜˜ ^
PosteriorSamples.cpp:82:42: warning: implicit conversion changes signedness: 'long' to 'size_type' (aka 'unsigned long') [-Wsign-conversion]
if(Sof(trSamples)!=N)trSamples.resize(N);
˜˜˜˜˜˜˜˜˜ ^
PosteriorSamples.cpp:85:16: warning: implicit conversion changes signedness: 'long' to 'size_type' (aka 'unsigned long') [-Wsign-conversion]
if(lines[tr]==-1){
˜˜˜˜˜ ^˜
PosteriorSamples.cpp:86:25: warning: implicit conversion changes signedness: 'long' to 'size_type' (aka 'unsigned long') [-Wsign-conversion]
for(i=0;lines[i+1]!=-1;i++);
˜˜˜˜˜ ˜^˜
PosteriorSamples.cpp:87:31: warning: implicit conversion changes signedness: 'long' to 'size_type' (aka 'unsigned long') [-Wsign-conversion]
samplesF.seekg(lines[i]);
˜˜˜˜˜ ^
PosteriorSamples.cpp:91:19: warning: implicit conversion changes signedness: 'long' to 'size_type' (aka 'unsigned long') [-Wsign-conversion]
lines[i]=samplesF.tellg();
˜˜˜˜˜ ^
PosteriorSamples.cpp:94:31: warning: implicit conversion changes signedness: 'long' to 'size_type' (aka 'unsigned long') [-Wsign-conversion]
samplesF.seekg(lines[tr]);
˜˜˜˜˜ ^˜
PosteriorSamples.cpp:97:30: warning: implicit conversion changes signedness: 'long' to 'size_type' (aka 'unsigned long') [-Wsign-conversion]
samplesF>>trSamples[i];
˜˜˜˜˜˜˜˜˜ ^
PosteriorSamples.cpp:99:20: warning: implicit conversion changes signedness: 'long' to 'size_type' (aka 'unsigned long') [-Wsign-conversion]
trSamples[i] *= norm;
˜˜˜˜˜˜˜˜˜ ^
PosteriorSamples.cpp:105:45: warning: implicit conversion changes signedness: 'long' to 'size_type' (aka 'unsigned long') [-Wsign-conversion]
if(lower(str)=="-inf")trSamples[i]=MINUS_INF;
˜˜˜˜˜˜˜˜˜ ^
PosteriorSamples.cpp:106:49: warning: implicit conversion changes signedness: 'long' to 'size_type' (aka 'unsigned long') [-Wsign-conversion]
else if(lower(str)=="nan")trSamples[i]=PLUS_INF;
˜˜˜˜˜˜˜˜˜ ^
PosteriorSamples.cpp:116:27: warning: implicit conversion changes signedness: 'long' to 'size_type' (aka 'unsigned long') [-Wsign-conversion]
trSamples = samples[tr];
˜˜˜˜˜˜˜ ^˜
PosteriorSamples.cpp:120:41: warning: implicit conversion changes signedness: 'long' to 'size_type' (aka 'unsigned long') [-Wsign-conversion]
for(long i=0;i<N;i++)trSamples[i] *= norm;
˜˜˜˜˜˜˜˜˜ ^
PosteriorSamples.cpp:141:18: warning: implicit conversion changes signedness: 'long' to 'size_type' (aka 'unsigned long') [-Wsign-conversion]
return cIndex[c].SS;
˜˜˜˜˜˜ ^
PosteriorSamples.cpp:153:19: warning: implicit conversion changes signedness: 'long' to 'size_type' (aka 'unsigned long') [-Wsign-conversion]
if(filesGot[i]=="C"){
˜˜˜˜˜˜˜˜ ^
PosteriorSamples.cpp:159:35: warning: implicit conversion changes signedness: 'long' to 'size_type' (aka 'unsigned long') [-Wsign-conversion]
files.push_back(filesGot[i]);
˜˜˜˜˜˜˜˜ ^
PosteriorSamples.cpp:170:19: warning: implicit conversion changes signedness: 'long' to 'size_type' (aka 'unsigned long') [-Wsign-conversion]
samples.resize(CN);
˜˜˜˜˜˜˜ ^˜
PosteriorSamples.cpp:171:14: warning: implicit conversion changes signedness: 'long' to 'size_type' (aka 'unsigned long') [-Wsign-conversion]
Ms.resize(CN);
˜˜ ^˜
PosteriorSamples.cpp:172:14: warning: implicit conversion changes signedness: 'long' to 'size_type' (aka 'unsigned long') [-Wsign-conversion]
Ns.resize(CN);
˜˜ ^˜
PosteriorSamples.cpp:181:20: warning: implicit conversion changes signedness: 'long' to 'size_type' (aka 'unsigned long') [-Wsign-conversion]
if(! samples[i].initSet(&Ms[i],&Ns[i],files[i])){
˜˜˜˜˜˜˜ ^
PosteriorSamples.cpp:181:35: warning: implicit conversion changes signedness: 'long' to 'size_type' (aka 'unsigned long') [-Wsign-conversion]
if(! samples[i].initSet(&Ms[i],&Ns[i],files[i])){
˜˜ ^
PosteriorSamples.cpp:181:42: warning: implicit conversion changes signedness: 'long' to 'size_type' (aka 'unsigned long') [-Wsign-conversion]
if(! samples[i].initSet(&Ms[i],&Ns[i],files[i])){
˜˜ ^
PosteriorSamples.cpp:181:51: warning: implicit conversion changes signedness: 'long' to 'size_type' (aka 'unsigned long') [-Wsign-conversion]
if(! samples[i].initSet(&Ms[i],&Ns[i],files[i])){
˜˜˜˜˜ ^
PosteriorSamples.cpp:182:63: warning: implicit conversion changes signedness: 'long' to 'size_type' (aka 'unsigned long') [-Wsign-conversion]
error("Conditions: file %s failed to open.\n",(files[i]).c_str());
˜˜˜˜˜ ^
PosteriorSamples.cpp:185:31: warning: implicit conversion changes signedness: 'long' to 'size_type' (aka 'unsigned long') [-Wsign-conversion]
if(areLogged != samples[i].logged()){
˜˜˜˜˜˜˜ ^
PosteriorSamples.cpp:186:101: warning: implicit conversion changes signedness: 'long' to 'size_type' (aka 'unsigned long') [-Wsign-conversion]
error("Conditions: Problem reading %s: some samples are logged and some are not.\n",(files[i]).c_str());
˜˜˜˜˜ ^
PosteriorSamples.cpp:189:16: warning: implicit conversion changes signedness: 'long' to 'size_type' (aka 'unsigned long') [-Wsign-conversion]
if(M!=Ms[i]){
˜˜ ^
PosteriorSamples.cpp:192:15: warning: implicit conversion changes signedness: 'long' to 'size_type' (aka 'unsigned long') [-Wsign-conversion]
if(N>Ns[i])N=Ns[i];
˜˜ ^
PosteriorSamples.cpp:192:23: warning: implicit conversion changes signedness: 'long' to 'size_type' (aka 'unsigned long') [-Wsign-conversion]
if(N>Ns[i])N=Ns[i];
˜˜ ^
PosteriorSamples.cpp:215:20: warning: implicit conversion changes signedness: 'long' to 'size_type' (aka 'unsigned long') [-Wsign-conversion]
trMap.resize(M,vector<long>(CN));
˜˜˜˜˜ ^
PosteriorSamples.cpp:215:35: warning: implicit conversion changes signedness: 'long' to 'size_type' (aka 'unsigned long') [-Wsign-conversion]
trMap.resize(M,vector<long>(CN));
˜˜˜˜˜˜ ^˜
PosteriorSamples.cpp:219:37: warning: implicit conversion changes signedness: 'long' to 'size_type' (aka 'unsigned long') [-Wsign-conversion]
if(j<CN)trFile >> trMap[i][j];
˜˜˜˜˜ ^
PosteriorSamples.cpp:219:40: warning: implicit conversion changes signedness: 'long' to 'size_type' (aka 'unsigned long') [-Wsign-conversion]
if(j<CN)trFile >> trMap[i][j];
˜˜˜˜˜ ^
PosteriorSamples.cpp:235:15: warning: implicit conversion changes signedness: 'long' to 'size_type' (aka 'unsigned long') [-Wsign-conversion]
samples[i].setNorm(norms[i]);
˜˜˜˜˜˜˜ ^
PosteriorSamples.cpp:235:32: warning: implicit conversion changes signedness: 'long' to 'size_type' (aka 'unsigned long') [-Wsign-conversion]
samples[i].setNorm(norms[i]);
˜˜˜˜˜ ^
PosteriorSamples.cpp:240:29: warning: implicit conversion changes signedness: 'long' to 'size_type' (aka 'unsigned long') [-Wsign-conversion]
if((cond>C)||(rep>cIndex[cond].SS)){
˜˜˜˜˜˜ ^˜˜˜
PosteriorSamples.cpp:244:36: warning: implicit conversion changes signedness: 'long' to 'size_type' (aka 'unsigned long') [-Wsign-conversion]
return getTranscript(rep+cIndex[cond].FF, tr, trSamples);
˜˜˜˜˜˜ ^˜˜˜
PosteriorSamples.cpp:257:27: warning: implicit conversion changes signedness: 'long' to 'size_type' (aka 'unsigned long') [-Wsign-conversion]
if(mapping) tr = trMap[tr][cond];
˜˜˜˜˜ ^˜
PosteriorSamples.cpp:257:31: warning: implicit conversion changes signedness: 'long' to 'size_type' (aka 'unsigned long') [-Wsign-conversion]
if(mapping) tr = trMap[tr][cond];
˜˜˜˜˜ ^˜˜˜
PosteriorSamples.cpp:258:15: warning: implicit conversion changes signedness: 'long' to 'size_type' (aka 'unsigned long') [-Wsign-conversion]
if(N != Ns[cond]){
˜˜ ^˜˜˜
PosteriorSamples.cpp:259:24: warning: implicit conversion changes signedness: 'long' to 'size_type' (aka 'unsigned long') [-Wsign-conversion]
status = samples[cond].getTranscript(tr, tmpSamples);
˜˜˜˜˜˜˜ ^˜˜˜
PosteriorSamples.cpp:260:47: warning: implicit conversion changes signedness: 'long' to 'size_type' (aka 'unsigned long') [-Wsign-conversion]
if(Sof(trSamples) != N)trSamples.resize(N);
˜˜˜˜˜˜˜˜˜ ^
PosteriorSamples.cpp:261:38: warning: implicit conversion changes signedness: 'long' to 'size_type' (aka 'unsigned long') [-Wsign-conversion]
for(long i=0;i<N;i++)trSamples[i] = tmpSamples[ getIndex(Ns[cond]) ];
˜˜˜˜˜˜˜˜˜ ^
PosteriorSamples.cpp:261:55: warning: implicit conversion changes signedness: 'long' to 'size_type' (aka 'unsigned long') [-Wsign-conversion]
for(long i=0;i<N;i++)trSamples[i] = tmpSamples[ getIndex(Ns[cond]) ];
˜˜˜˜˜˜˜˜˜˜ ^˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜
PosteriorSamples.cpp:261:67: warning: implicit conversion changes signedness: 'long' to 'size_type' (aka 'unsigned long') [-Wsign-conversion]
for(long i=0;i<N;i++)trSamples[i] = tmpSamples[ getIndex(Ns[cond]) ];
˜˜ ^˜˜˜
PosteriorSamples.cpp:263:24: warning: implicit conversion changes signedness: 'long' to 'size_type' (aka 'unsigned long') [-Wsign-conversion]
status = samples[cond].getTranscript(tr, trSamples);
˜˜˜˜˜˜˜ ^˜˜˜
PosteriorSamples.cpp:278:21: warning: implicit conversion changes signedness: 'long' to 'size_type' (aka 'unsigned long') [-Wsign-conversion]
if(samplesN > Ns[cond]){
˜˜ ^˜˜˜
PosteriorSamples.cpp:286:24: warning: implicit conversion changes signedness: 'long' to 'size_type' (aka 'unsigned long') [-Wsign-conversion]
if(mapping)tr=trMap[tr][cond];
˜˜˜˜˜ ^˜
PosteriorSamples.cpp:286:28: warning: implicit conversion changes signedness: 'long' to 'size_type' (aka 'unsigned long') [-Wsign-conversion]
if(mapping)tr=trMap[tr][cond];
˜˜˜˜˜ ^˜˜˜
PosteriorSamples.cpp:287:22: warning: implicit conversion changes signedness: 'long' to 'size_type' (aka 'unsigned long') [-Wsign-conversion]
if(samplesN != Ns[cond]){
˜˜ ^˜˜˜
PosteriorSamples.cpp:288:24: warning: implicit conversion changes signedness: 'long' to 'size_type' (aka 'unsigned long') [-Wsign-conversion]
status = samples[cond].getTranscript(tr, tmpSamples);
˜˜˜˜˜˜˜ ^˜˜˜
PosteriorSamples.cpp:289:54: warning: implicit conversion changes signedness: 'long' to 'size_type' (aka 'unsigned long') [-Wsign-conversion]
if(Sof(trSamples) != samplesN)trSamples.resize(samplesN);
˜˜˜˜˜˜˜˜˜ ^˜˜˜˜˜˜˜
PosteriorSamples.cpp:291:20: warning: implicit conversion changes signedness: 'long' to 'size_type' (aka 'unsigned long') [-Wsign-conversion]
trSamples[i] = tmpSamples[ getIndex(Ns[cond]) ];
˜˜˜˜˜˜˜˜˜ ^
PosteriorSamples.cpp:291:37: warning: implicit conversion changes signedness: 'long' to 'size_type' (aka 'unsigned long') [-Wsign-conversion]
trSamples[i] = tmpSamples[ getIndex(Ns[cond]) ];
˜˜˜˜˜˜˜˜˜˜ ^˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜
PosteriorSamples.cpp:291:49: warning: implicit conversion changes signedness: 'long' to 'size_type' (aka 'unsigned long') [-Wsign-conversion]
trSamples[i] = tmpSamples[ getIndex(Ns[cond]) ];
˜˜ ^˜˜˜
PosteriorSamples.cpp:293:24: warning: implicit conversion changes signedness: 'long' to 'size_type' (aka 'unsigned long') [-Wsign-conversion]
status = samples[cond].getTranscript(tr, trSamples);
˜˜˜˜˜˜˜ ^˜˜˜
PosteriorSamples.cpp:299:15: warning: implicit conversion changes signedness: 'long' to 'size_type' (aka 'unsigned long') [-Wsign-conversion]
samples[i].close();
˜˜˜˜˜˜˜ ^
65 warnings generated.
clang++ -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -DPACKAGE_NAME=\"Bitseq\" -DPACKAGE_TARNAME=\"bitseq\" -DPACKAGE_VERSION=\"1.4.x\" -DPACKAGE_STRING=\"Bitseq\ 1.4.x\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DBS_VERSION=\"1.4.2\" -DBIOC_BUILD=1 -D_USE_KNETFILE -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -I/usr/local/include -I"/Library/Frameworks/R.framework/Versions/3.0/Resources/library/Rsamtools/include" -I"/Library/Frameworks/R.framework/Versions/3.0/Resources/library/zlibbioc/include" -I. -fPIC -mtune=native -g -O2 -Wall -pedantic -Wconversion -c R_init_BitSeq.cpp -o R_init_BitSeq.o
clang++ -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -DPACKAGE_NAME=\"Bitseq\" -DPACKAGE_TARNAME=\"bitseq\" -DPACKAGE_VERSION=\"1.4.x\" -DPACKAGE_STRING=\"Bitseq\ 1.4.x\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DBS_VERSION=\"1.4.2\" -DBIOC_BUILD=1 -D_USE_KNETFILE -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -I/usr/local/include -I"/Library/Frameworks/R.framework/Versions/3.0/Resources/library/Rsamtools/include" -I"/Library/Frameworks/R.framework/Versions/3.0/Resources/library/zlibbioc/include" -I. -fPIC -mtune=native -g -O2 -Wall -pedantic -Wconversion -c ReadDistribution.cpp -o ReadDistribution.o
In file included from ReadDistribution.cpp:6:
./common.h:17:17: warning: variadic macros are a C99 feature [-Wvariadic-macros]
#define message(...) Rprintf(__VA_ARGS__)
^
In file included from ReadDistribution.cpp:8:
./MyTimer.h:28:20: warning: implicit conversion changes signedness: 'long' to 'size_type' (aka 'unsigned long') [-Wsign-conversion]
times.resize(N);
˜˜˜˜˜ ^
./MyTimer.h:36:23: warning: implicit conversion changes signedness: 'long' to 'size_type' (aka 'unsigned long') [-Wsign-conversion]
times.resize(N);
˜˜˜˜˜ ^
./MyTimer.h:38:13: warning: implicit conversion changes signedness: 'long' to 'size_type' (aka 'unsigned long') [-Wsign-conversion]
times[timer]=time(NULL);
˜˜˜˜˜ ^˜˜˜˜
./MyTimer.h:43:28: warning: implicit conversion changes signedness: 'long' to 'size_type' (aka 'unsigned long') [-Wsign-conversion]
ret=time(NULL)-times[timer];
˜˜˜˜˜ ^˜˜˜˜
./MyTimer.h:46:13: warning: implicit conversion changes signedness: 'long' to 'size_type' (aka 'unsigned long') [-Wsign-conversion]
times[timer]=time(NULL);
˜˜˜˜˜ ^˜˜˜˜
./MyTimer.h:52:28: warning: implicit conversion changes signedness: 'long' to 'size_type' (aka 'unsigned long') [-Wsign-conversion]
ret=time(NULL)-times[timer];
˜˜˜˜˜ ^˜˜˜˜
./MyTimer.h:60:28: warning: implicit conversion changes signedness: 'long' to 'size_type' (aka 'unsigned long') [-Wsign-conversion]
ret=time(NULL)-times[timer];
˜˜˜˜˜ ^˜˜˜˜
./MyTimer.h:63:13: warning: implicit conversion changes signedness: 'long' to 'size_type' (aka 'unsigned long') [-Wsign-conversion]
times[timer]=time(NULL);
˜˜˜˜˜ ^˜˜˜˜
In file included from ReadDistribution.cpp:9:
In file included from ./ReadDistribution.h:10:
./TranscriptSequence.h:55:27: warning: implicit conversion changes signedness: 'size_type' (aka 'unsigned long') to 'long' [-Wsign-conversion]
long getG(){ return geneNames.size(); }
˜˜˜˜˜˜ ^˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜
In file included from ReadDistribution.cpp:9:
In file included from ./ReadDistribution.h:11:
./TranscriptExpression.h:32:38: warning: implicit conversion changes signedness: 'long' to 'size_type' (aka 'unsigned long') [-Wsign-conversion]
double exp(long tr){return trs[tr].exp;}
˜˜˜ ^˜
./TranscriptExpression.h:33:38: warning: implicit conversion changes signedness: 'long' to 'size_type' (aka 'unsigned long') [-Wsign-conversion]
double var(long tr){return trs[tr].var;}
˜˜˜ ^˜
./TranscriptExpression.h:34:35: warning: implicit conversion changes signedness: 'long' to 'size_type' (aka 'unsigned long') [-Wsign-conversion]
long id(long tr){return trs[tr].id;}
˜˜˜ ^˜
ReadDistribution.cpp:99:23: warning: implicit conversion changes signedness: 'long' to 'size_type' (aka 'unsigned long') [-Wsign-conversion]
trFragSeen5.resize(M);
˜˜˜˜˜˜˜˜˜˜˜ ^
ReadDistribution.cpp:100:23: warning: implicit conversion changes signedness: 'long' to 'size_type' (aka 'unsigned long') [-Wsign-conversion]
trFragSeen3.resize(M);
˜˜˜˜˜˜˜˜˜˜˜ ^
ReadDistribution.cpp:101:52: warning: implicit conversion changes signedness: 'long' to 'size_type' (aka 'unsigned long') [-Wsign-conversion]
weightNorms.resize(3,vector<map<long, double> >(M));
˜˜˜˜˜˜ ^
ReadDistribution.cpp:108:18: warning: implicit conversion changes signedness: 'long' to 'size_type' (aka 'unsigned long') [-Wsign-conversion]
seqProb[j].push_back(VlmmNode(vlmmNodeDependence[i]));
˜˜˜˜˜˜˜ ^
ReadDistribution.cpp:200:29: warning: implicit conversion changes signedness: 'long' to 'size_type' (aka 'unsigned long') [-Wsign-conversion]
mapAdd(trFragSeen5[tid], (long)len, Iexp);
˜˜˜˜˜˜˜˜˜˜˜ ^˜˜
ReadDistribution.cpp:205:29: warning: implicit conversion changes signedness: 'long' to 'size_type' (aka 'unsigned long') [-Wsign-conversion]
mapAdd(trFragSeen3[tid], (long)len, Iexp);
˜˜˜˜˜˜˜˜˜˜˜ ^˜˜
ReadDistribution.cpp:210:26: warning: implicit conversion changes signedness: 'long' to 'size_type' (aka 'unsigned long') [-Wsign-conversion]
mapAdd(trFragSeen3[tid], (long)len, Iexp);
˜˜˜˜˜˜˜˜˜˜˜ ^˜˜
ReadDistribution.cpp:214:26: warning: implicit conversion changes signedness: 'long' to 'size_type' (aka 'unsigned long') [-Wsign-conversion]
mapAdd(trFragSeen5[tid], (long)len, Iexp);
˜˜˜˜˜˜˜˜˜˜˜ ^˜˜
ReadDistribution.cpp:253:28: warning: implicit conversion changes signedness: 'long' to 'size_type' (aka 'unsigned long') [-Wsign-conversion]
for( mIt=trFragSeen3[m].begin(); mIt != trFragSeen3[m].end(); mIt++){
˜˜˜˜˜˜˜˜˜˜˜ ^
ReadDistribution.cpp:253:59: warning: implicit conversion changes signedness: 'long' to 'size_type' (aka 'unsigned long') [-Wsign-conversion]
for( mIt=trFragSeen3[m].begin(); mIt != trFragSeen3[m].end(); mIt++){
˜˜˜˜˜˜˜˜˜˜˜ ^
ReadDistribution.cpp:260:36: warning: implicit conversion changes signedness: 'long' to 'size_type' (aka 'unsigned long') [-Wsign-conversion]
posProb[uniformM_3][group][trNumberOfBins -1 -i]+= Iexp * ((double)(i+1)*trLen / trNumberOfBins - fragLen + 1);
˜˜˜˜˜˜˜ ^˜˜˜˜
ReadDistribution.cpp:260:61: warning: implicit conversion changes signedness: 'long' to 'size_type' (aka 'unsigned long') [-Wsign-conversion]
posProb[uniformM_3][group][trNumberOfBins -1 -i]+= Iexp * ((double)(i+1)*trLen / trNumberOfBins - fragLen + 1);
˜˜˜˜˜˜˜ ˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜^˜
ReadDistribution.cpp:262:36: warning: implicit conversion changes signedness: 'long' to 'size_type' (aka 'unsigned long') [-Wsign-conversion]
posProb[uniformM_3][group][trNumberOfBins -1 -i]+= Iexp * ((double)trLen / trNumberOfBins);
˜˜˜˜˜˜˜ ^˜˜˜˜
ReadDistribution.cpp:262:61: warning: implicit conversion changes signedness: 'long' to 'size_type' (aka 'unsigned long') [-Wsign-conversion]
posProb[uniformM_3][group][trNumberOfBins -1 -i]+= Iexp * ((double)trLen / trNumberOfBins);
˜˜˜˜˜˜˜ ˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜^˜
ReadDistribution.cpp:267:28: warning: implicit conversion changes signedness: 'long' to 'size_type' (aka 'unsigned long') [-Wsign-conversion]
for( mIt=trFragSeen5[m].begin(); mIt != trFragSeen5[m].end(); mIt++){
˜˜˜˜˜˜˜˜˜˜˜ ^
ReadDistribution.cpp:267:59: warning: implicit conversion changes signedness: 'long' to 'size_type' (aka 'unsigned long') [-Wsign-conversion]
for( mIt=trFragSeen5[m].begin(); mIt != trFragSeen5[m].end(); mIt++){
˜˜˜˜˜˜˜˜˜˜˜ ^
ReadDistribution.cpp:274:36: warning: implicit conversion changes signedness: 'long' to 'size_type' (aka 'unsigned long') [-Wsign-conversion]
posProb[uniformM_5][group][i]+= Iexp * ((double)(i+1)*trLen / trNumberOfBins - fragLen + 1);
˜˜˜˜˜˜˜ ^˜˜˜˜
ReadDistribution.cpp:274:43: warning: implicit conversion changes signedness: 'long' to 'size_type' (aka 'unsigned long') [-Wsign-conversion]
posProb[uniformM_5][group][i]+= Iexp * ((double)(i+1)*trLen / trNumberOfBins - fragLen + 1);
˜˜˜˜˜˜˜ ^
ReadDistribution.cpp:276:36: warning: implicit conversion changes signedness: 'long' to 'size_type' (aka 'unsigned long') [-Wsign-conversion]
posProb[uniformM_5][group][i]+= Iexp * ((double)trLen / trNumberOfBins);
˜˜˜˜˜˜˜ ^˜˜˜˜
ReadDistribution.cpp:276:43: warning: implicit conversion changes signedness: 'long' to 'size_type' (aka 'unsigned long') [-Wsign-conversion]
posProb[uniformM_5][group][i]+= Iexp * ((double)trLen / trNumberOfBins);
˜˜˜˜˜˜˜ ^
ReadDistribution.cpp:285:55: warning: implicit conversion changes signedness: 'long' to 'size_type' (aka 'unsigned long') [-Wsign-conversion]
for(i=0;i<trNumberOfBins;i++)norm += posProb[j][group][i];
˜˜˜˜˜˜˜ ^
ReadDistribution.cpp:285:58: warning: implicit conversion changes signedness: 'long' to 'size_type' (aka 'unsigned long') [-Wsign-conversion]
for(i=0;i<trNumberOfBins;i++)norm += posProb[j][group][i];
˜˜˜˜˜˜˜ ^˜˜˜˜
ReadDistribution.cpp:285:65: warning: implicit conversion changes signedness: 'long' to 'size_type' (aka 'unsigned long') [-Wsign-conversion]
for(i=0;i<trNumberOfBins;i++)norm += posProb[j][group][i];
˜˜˜˜˜˜˜ ^
ReadDistribution.cpp:286:47: warning: implicit conversion changes signedness: 'long' to 'size_type' (aka 'unsigned long') [-Wsign-conversion]
for(i=0;i<trNumberOfBins;i++)posProb[j][group][i] /= norm;
˜˜˜˜˜˜˜ ^
ReadDistribution.cpp:286:50: warning: implicit conversion changes signedness: 'long' to 'size_type' (aka 'unsigned long') [-Wsign-conversion]
for(i=0;i<trNumberOfBins;i++)posProb[j][group][i] /= norm;
˜˜˜˜˜˜˜ ^˜˜˜˜
ReadDistribution.cpp:286:57: warning: implicit conversion changes signedness: 'long' to 'size_type' (aka 'unsigned long') [-Wsign-conversion]
for(i=0;i<trNumberOfBins;i++)posProb[j][group][i] /= norm;
˜˜˜˜˜˜˜ ^
ReadDistribution.cpp:291:28: warning: implicit conversion changes signedness: 'long' to 'size_type' (aka 'unsigned long') [-Wsign-conversion]
posProb[weight_5][group][i] = posProb[readM_5][group][i]/posProb[uniformM_5][group][i];
˜˜˜˜˜˜˜ ^˜˜˜˜
ReadDistribution.cpp:291:35: warning: implicit conversion changes signedness: 'long' to 'size_type' (aka 'unsigned long') [-Wsign-conversion]
posProb[weight_5][group][i] = posProb[readM_5][group][i]/posProb[uniformM_5][group][i];
˜˜˜˜˜˜˜ ^
ReadDistribution.cpp:291:57: warning: implicit conversion changes signedness: 'long' to 'size_type' (aka 'unsigned long') [-Wsign-conversion]
posProb[weight_5][group][i] = posProb[readM_5][group][i]/posProb[uniformM_5][group][i];
˜˜˜˜˜˜˜ ^˜˜˜˜
ReadDistribution.cpp:291:64: warning: implicit conversion changes signedness: 'long' to 'size_type' (aka 'unsigned long') [-Wsign-conversion]
posProb[weight_5][group][i] = posProb[readM_5][group][i]/posProb[uniformM_5][group][i];
˜˜˜˜˜˜˜ ^
ReadDistribution.cpp:291:87: warning: implicit conversion changes signedness: 'long' to 'size_type' (aka 'unsigned long') [-Wsign-conversion]
posProb[weight_5][group][i] = posProb[readM_5][group][i]/posProb[uniformM_5][group][i];
˜˜˜˜˜˜˜ ^˜˜˜˜
ReadDistribution.cpp:291:94: warning: implicit conversion changes signedness: 'long' to 'size_type' (aka 'unsigned long') [-Wsign-conversion]
posProb[weight_5][group][i] = posProb[readM_5][group][i]/posProb[uniformM_5][group][i];
˜˜˜˜˜˜˜ ^
ReadDistribution.cpp:293:28: warning: implicit conversion changes signedness: 'long' to 'size_type' (aka 'unsigned long') [-Wsign-conversion]
posProb[weight_3][group][i] = posProb[readM_3][group][i]/posProb[uniformM_3][group][i];
˜˜˜˜˜˜˜ ^˜˜˜˜
ReadDistribution.cpp:293:35: warning: implicit conversion changes signedness: 'long' to 'size_type' (aka 'unsigned long') [-Wsign-conversion]
posProb[weight_3][group][i] = posProb[readM_3][group][i]/posProb[uniformM_3][group][i];
˜˜˜˜˜˜˜ ^
ReadDistribution.cpp:293:57: warning: implicit conversion changes signedness: 'long' to 'size_type' (aka 'unsigned long') [-Wsign-conversion]
posProb[weight_3][group][i] = posProb[readM_3][group][i]/posProb[uniformM_3][group][i];
˜˜˜˜˜˜˜ ^˜˜˜˜
ReadDistribution.cpp:293:64: warning: implicit conversion changes signedness: 'long' to 'size_type' (aka 'unsigned long') [-Wsign-conversion]
posProb[weight_3][group][i] = posProb[readM_3][group][i]/posProb[uniformM_3][group][i];
˜˜˜˜˜˜˜ ^
ReadDistribution.cpp:293:87: warning: implicit conversion changes signedness: 'long' to 'size_type' (aka 'unsigned long') [-Wsign-conversion]
posProb[weight_3][group][i] = posProb[readM_3][group][i]/posProb[uniformM_3][group][i];
˜˜˜˜˜˜˜ ^˜˜˜˜
ReadDistribution.cpp:293:94: warning: implicit conversion changes signedness: 'long' to 'size_type' (aka 'unsigned long') [-Wsign-conversion]
posProb[weight_3][group][i] = posProb[readM_3][group][i]/posProb[uniformM_3][group][i];
˜˜˜˜˜˜˜ ^
ReadDistribution.cpp:305:27: warning: implicit conversion changes signedness: 'long' to 'size_type' (aka 'unsigned long') [-Wsign-conversion]
for(mIt=trFragSeen3[m].begin();mIt!= trFragSeen3[m].end();mIt++)
˜˜˜˜˜˜˜˜˜˜˜ ^
ReadDistribution.cpp:305:56: warning: implicit conversion changes signedness: 'long' to 'size_type' (aka 'unsigned long') [-Wsign-conversion]
for(mIt=trFragSeen3[m].begin();mIt!= trFragSeen3[m].end();mIt++)
˜˜˜˜˜˜˜˜˜˜˜ ^
ReadDistribution.cpp:308:24: warning: implicit conversion changes signedness: 'long' to 'size_type' (aka 'unsigned long') [-Wsign-conversion]
mItR=trFragSeen3[m].rbegin();
˜˜˜˜˜˜˜˜˜˜˜ ^
ReadDistribution.cpp:309:23: warning: implicit conversion changes signedness: 'long' to 'size_type' (aka 'unsigned long') [-Wsign-conversion]
mIt=trFragSeen5[m].begin();
˜˜˜˜˜˜˜˜˜˜˜ ^
ReadDistribution.cpp:312:34: warning: implicit conversion changes signedness: 'long' to 'size_type' (aka 'unsigned long') [-Wsign-conversion]
while((mIt!=trFragSeen5[m].end())&&(mIt->first <= p+1)){IexpSum5+=mIt->second/ (trLen - mIt->first + 1); mIt++;}
˜˜˜˜˜˜˜˜˜˜˜ ^
ReadDistribution.cpp:313:35: warning: implicit conversion changes signedness: 'long' to 'size_type' (aka 'unsigned long') [-Wsign-conversion]
while((mItR!=trFragSeen3[m].rend())&&(trLen-p < mItR->first)){IexpSum3-= mItR->second / (trLen - mItR->first + 1) ; mItR++;}
˜˜˜˜˜˜˜˜˜˜˜ ^
ReadDistribution.cpp:322:18: warning: implicit conversion changes signedness: 'long' to 'size_type' (aka 'unsigned long') [-Wsign-conversion]
seqProb[j][i].normalize();
˜˜˜˜˜˜˜ ^
ReadDistribution.cpp:322:21: warning: implicit conversion changes signedness: 'long' to 'size_type' (aka 'unsigned long') [-Wsign-conversion]
seqProb[j][i].normalize();
˜˜˜˜˜˜˜ ^
ReadDistribution.cpp:337:24: warning: implicit conversion changes signedness: 'long' to 'size_type' (aka 'unsigned long') [-Wsign-conversion]
outF<<seqProb[j][i].getPsum('A')<<" "<<seqProb[j][i].getPsum('C')<<" "<<seqProb[j][i].getPsum('G')<<" "<<seqProb[j][i].getPsum('T')<<endl;
˜˜˜˜˜˜˜ ^
ReadDistribution.cpp:337:27: warning: implicit conversion changes signedness: 'long' to 'size_type' (aka 'unsigned long') [-Wsign-conversion]
outF<<seqProb[j][i].getPsum('A')<<" "<<seqProb[j][i].getPsum('C')<<" "<<seqProb[j][i].getPsum('G')<<" "<<seqProb[j][i].getPsum('T')<<endl;
˜˜˜˜˜˜˜ ^
ReadDistribution.cpp:337:57: warning: implicit conversion changes signedness: 'long' to 'size_type' (aka 'unsigned long') [-Wsign-conversion]
outF<<seqProb[j][i].getPsum('A')<<" "<<seqProb[j][i].getPsum('C')<<" "<<seqProb[j][i].getPsum('G')<<" "<<seqProb[j][i].getPsum('T')<<endl;
˜˜˜˜˜˜˜ ^
ReadDistribution.cpp:337:60: warning: implicit conversion changes signedness: 'long' to 'size_type' (aka 'unsigned long') [-Wsign-conversion]
outF<<seqProb[j][i].getPsum('A')<<" "<<seqProb[j][i].getPsum('C')<<" "<<seqProb[j][i].getPsum('G')<<" "<<seqProb[j][i].getPsum('T')<<endl;
˜˜˜˜˜˜˜ ^
ReadDistribution.cpp:337:90: warning: implicit conversion changes signedness: 'long' to 'size_type' (aka 'unsigned long') [-Wsign-conversion]
outF<<seqProb[j][i].getPsum('A')<<" "<<seqProb[j][i].getPsum('C')<<" "<<seqProb[j][i].getPsum('G')<<" "<<seqProb[j][i].getPsum('T')<<endl;
˜˜˜˜˜˜˜ ^
ReadDistribution.cpp:337:93: warning: implicit conversion changes signedness: 'long' to 'size_type' (aka 'unsigned long') [-Wsign-conversion]
outF<<seqProb[j][i].getPsum('A')<<" "<<seqProb[j][i].getPsum('C')<<" "<<seqProb[j][i].getPsum('G')<<" "<<seqProb[j][i].getPsum('T')<<endl;
˜˜˜˜˜˜˜ ^
ReadDistribution.cpp:337:123: warning: implicit conversion changes signedness: 'long' to 'size_type' (aka 'unsigned long') [-Wsign-conversion]
outF<<seqProb[j][i].getPsum('A')<<" "<<seqProb[j][i].getPsum('C')<<" "<<seqProb[j][i].getPsum('G')<<" "<<seqProb[j][i].getPsum('T')<<endl;
˜˜˜˜˜˜˜ ^
ReadDistribution.cpp:337:126: warning: implicit conversion changes signedness: 'long' to 'size_type' (aka 'unsigned long') [-Wsign-conversion]
outF<<seqProb[j][i].getPsum('A')<<" "<<seqProb[j][i].getPsum('C')<<" "<<seqProb[j][i].getPsum('G')<<" "<<seqProb[j][i].getPsum('T')<<endl;
˜˜˜˜˜˜˜ ^
ReadDistribution.cpp:346:27: warning: implicit conversion changes signedness: 'long' to 'size_type' (aka 'unsigned long') [-Wsign-conversion]
outF<<posProb[j][g][i]<<" ";
˜˜˜˜˜˜˜ ^
ReadDistribution.cpp:346:30: warning: implicit conversion changes signedness: 'long' to 'size_type' (aka 'unsigned long') [-Wsign-conversion]
outF<<posProb[j][g][i]<<" ";
˜˜˜˜˜˜˜ ^
ReadDistribution.cpp:346:33: warning: implicit conversion changes signedness: 'long' to 'size_type' (aka 'unsigned long') [-Wsign-conversion]
outF<<posProb[j][g][i]<<" ";
˜˜˜˜˜˜˜ ^
ReadDistribution.cpp:392:30: warning: implicit conversion changes signedness: 'long' to 'size_type' (aka 'unsigned long') [-Wsign-conversion]
if((base2int(seq[i]) == -1)||
˜˜˜ ^
ReadDistribution.cpp:393:30: warning: implicit conversion changes signedness: 'long' to 'size_type' (aka 'unsigned long') [-Wsign-conversion]
(base2int(seq[i]) != bamBase2int(bam1_seqi(bam1_seq(samA),j))))misses--;
˜˜˜ ^
ReadDistribution.cpp:422:24: warning: implicit conversion changes signedness: 'long' to 'size_type' (aka 'unsigned long') [-Wsign-conversion]
if((base2int(seq[i]) == -1)||(base2int(seq[i]) != bamBase2int(bam1_seqi(bam1_seq(samA),j)))){
˜˜˜ ^
ReadDistribution.cpp:422:50: warning: implicit conversion changes signedness: 'long' to 'size_type' (aka 'unsigned long') [-Wsign-conversion]
if((base2int(seq[i]) == -1)||(base2int(seq[i]) != bamBase2int(bam1_seqi(bam1_seq(samA),j)))){
˜˜˜ ^
ReadDistribution.cpp:546:19: warning: implicit conversion changes signedness: 'long' to 'size_type' (aka 'unsigned long') [-Wsign-conversion]
posProb[bias][ group ][ rel ] += Iexp;
˜˜˜˜˜˜˜ ^˜˜˜˜
ReadDistribution.cpp:546:28: warning: implicit conversion changes signedness: 'long' to 'size_type' (aka 'unsigned long') [-Wsign-conversion]
posProb[bias][ group ][ rel ] += Iexp;
˜˜˜˜˜˜˜ ^˜˜
ReadDistribution.cpp:562:21: warning: implicit conversion changes signedness: 'long' to 'size_type' (aka 'unsigned long') [-Wsign-conversion]
seqProb[bias][i].update( Iexp, seq[i+2], seq[i+1], seq[i]);
˜˜˜˜˜˜˜ ^
ReadDistribution.cpp:562:43: warning: implicit conversion changes signedness: 'long' to 'size_type' (aka 'unsigned long') [-Wsign-conversion]
seqProb[bias][i].update( Iexp, seq[i+2], seq[i+1], seq[i]);
˜˜˜ ˜^˜
ReadDistribution.cpp:562:53: warning: implicit conversion changes signedness: 'long' to 'size_type' (aka 'unsigned long') [-Wsign-conversion]
seqProb[bias][i].update( Iexp, seq[i+2], seq[i+1], seq[i]);
˜˜˜ ˜^˜
ReadDistribution.cpp:562:62: warning: implicit conversion changes signedness: 'long' to 'size_type' (aka 'unsigned long') [-Wsign-conversion]
seqProb[bias][i].update( Iexp, seq[i+2], seq[i+1], seq[i]);
˜˜˜ ^
ReadDistribution.cpp:579:35: warning: implicit conversion changes signedness: 'long' to 'size_type' (aka 'unsigned long') [-Wsign-conversion]
return posProb[ weight_5 ][ group ][ rel ];
˜˜˜˜˜˜˜ ^˜˜˜˜
ReadDistribution.cpp:579:44: warning: implicit conversion changes signedness: 'long' to 'size_type' (aka 'unsigned long') [-Wsign-conversion]
return posProb[ weight_5 ][ group ][ rel ];
˜˜˜˜˜˜˜ ^˜˜
ReadDistribution.cpp:581:35: warning: implicit conversion changes signedness: 'long' to 'size_type' (aka 'unsigned long') [-Wsign-conversion]
return posProb[ weight_3 ][ group ][ rel ];
˜˜˜˜˜˜˜ ^˜˜˜˜
ReadDistribution.cpp:581:44: warning: implicit conversion changes signedness: 'long' to 'size_type' (aka 'unsigned long') [-Wsign-conversion]
return posProb[ weight_3 ][ group ][ rel ];
˜˜˜˜˜˜˜ ^˜˜
ReadDistribution.cpp:595:9: warning: unknown pragma ignored [-Wunknown-pragmas]
#pragma omp critical
^
ReadDistribution.cpp:601:32: warning: implicit conversion changes signedness: 'long' to 'size_type' (aka 'unsigned long') [-Wsign-conversion]
B *= seqProb[readM_3][i].getP( seq[i+2], seq[i+1], seq[i]) /
˜˜˜˜˜˜˜ ^
ReadDistribution.cpp:601:46: warning: implicit conversion changes signedness: 'long' to 'size_type' (aka 'unsigned long') [-Wsign-conversion]
B *= seqProb[readM_3][i].getP( seq[i+2], seq[i+1], seq[i]) /
˜˜˜ ˜^˜
ReadDistribution.cpp:601:56: warning: implicit conversion changes signedness: 'long' to 'size_type' (aka 'unsigned long') [-Wsign-conversion]
B *= seqProb[readM_3][i].getP( seq[i+2], seq[i+1], seq[i]) /
˜˜˜ ˜^˜
ReadDistribution.cpp:601:65: warning: implicit conversion changes signedness: 'long' to 'size_type' (aka 'unsigned long') [-Wsign-conversion]
B *= seqProb[readM_3][i].getP( seq[i+2], seq[i+1], seq[i]) /
˜˜˜ ^
ReadDistribution.cpp:602:35: warning: implicit conversion changes signedness: 'long' to 'size_type' (aka 'unsigned long') [-Wsign-conversion]
seqProb[uniformM_3][i].getP( seq[i+2], seq[i+1], seq[i]);
˜˜˜˜˜˜˜ ^
ReadDistribution.cpp:602:49: warning: implicit conversion changes signedness: 'long' to 'size_type' (aka 'unsigned long') [-Wsign-conversion]
seqProb[uniformM_3][i].getP( seq[i+2], seq[i+1], seq[i]);
˜˜˜ ˜^˜
ReadDistribution.cpp:602:59: warning: implicit conversion changes signedness: 'long' to 'size_type' (aka 'unsigned long') [-Wsign-conversion]
seqProb[uniformM_3][i].getP( seq[i+2], seq[i+1], seq[i]);
˜˜˜ ˜^˜
ReadDistribution.cpp:602:68: warning: implicit conversion changes signedness: 'long' to 'size_type' (aka 'unsigned long') [-Wsign-conversion]
seqProb[uniformM_3][i].getP( seq[i+2], seq[i+1], seq[i]);
˜˜˜ ^
ReadDistribution.cpp:604:9: warning: unknown pragma ignored [-Wunknown-pragmas]
#pragma omp critical
^
ReadDistribution.cpp:610:32: warning: implicit conversion changes signedness: 'long' to 'size_type' (aka 'unsigned long') [-Wsign-conversion]
B *= seqProb[readM_5][i].getP( seq[i+2], seq[i+1], seq[i]) /
˜˜˜˜˜˜˜ ^
ReadDistribution.cpp:610:46: warning: implicit conversion changes signedness: 'long' to 'size_type' (aka 'unsigned long') [-Wsign-conversion]
B *= seqProb[readM_5][i].getP( seq[i+2], seq[i+1], seq[i]) /
˜˜˜ ˜^˜
ReadDistribution.cpp:610:56: warning: implicit conversion changes signedness: 'long' to 'size_type' (aka 'unsigned long') [-Wsign-conversion]
B *= seqProb[readM_5][i].getP( seq[i+2], seq[i+1], seq[i]) /
˜˜˜ ˜^˜
ReadDistribution.cpp:610:65: warning: implicit conversion changes signedness: 'long' to 'size_type' (aka 'unsigned long') [-Wsign-conversion]
B *= seqProb[readM_5][i].getP( seq[i+2], seq[i+1], seq[i]) /
˜˜˜ ^
ReadDistribution.cpp:611:35: warning: implicit conversion changes signedness: 'long' to 'size_type' (aka 'unsigned long') [-Wsign-conversion]
seqProb[uniformM_5][i].getP( seq[i+2], seq[i+1], seq[i]);
˜˜˜˜˜˜˜ ^
ReadDistribution.cpp:611:49: warning: implicit conversion changes signedness: 'long' to 'size_type' (aka 'unsigned long') [-Wsign-conversion]
seqProb[uniformM_5][i].getP( seq[i+2], seq[i+1], seq[i]);
˜˜˜ ˜^˜
ReadDistribution.cpp:611:59: warning: implicit conversion changes signedness: 'long' to 'size_type' (aka 'unsigned long') [-Wsign-conversion]
seqProb[uniformM_5][i].getP( seq[i+2], seq[i+1], seq[i]);
˜˜˜ ˜^˜
ReadDistribution.cpp:611:68: warning: implicit conversion changes signedness: 'long' to 'size_type' (aka 'unsigned long') [-Wsign-conversion]
seqProb[uniformM_5][i].getP( seq[i+2], seq[i+1], seq[i]);
˜˜˜ ^
ReadDistribution.cpp:617:25: warning: implicit conversion changes signedness: 'long' to 'size_type' (aka 'unsigned long') [-Wsign-conversion]
if(weightNorms[read][tid].count(len) == 0){
˜˜˜˜˜˜˜˜˜˜˜ ^˜˜
ReadDistribution.cpp:620:9: warning: unknown pragma ignored [-Wunknown-pragmas]
#pragma omp parallel for private(w) reduction(+:norm)
^
ReadDistribution.cpp:631:25: warning: implicit conversion changes signedness: 'long' to 'size_type' (aka 'unsigned long') [-Wsign-conversion]
weightNorms[read][tid][len] = norm;
˜˜˜˜˜˜˜˜˜˜˜ ^˜˜
ReadDistribution.cpp:635:29: warning: implicit conversion changes signedness: 'long' to 'size_type' (aka 'unsigned long') [-Wsign-conversion]
return weightNorms[read][tid][len];
˜˜˜˜˜˜˜˜˜˜˜ ^˜˜
ReadDistribution.cpp:652:24: warning: implicit conversion changes signedness: 'long' to 'size_type' (aka 'unsigned long') [-Wsign-conversion]
vector<double> effL(M,0);
˜˜˜˜ ^
ReadDistribution.cpp:657:9: warning: unknown pragma ignored [-Wunknown-pragmas]
#pragma omp parallel for private(len,trLen,pos,eL,lenP,wNorm,lCdfNorm)
^
ReadDistribution.cpp:660:9: warning: unknown pragma ignored [-Wunknown-pragmas]
#pragma omp critical
^
ReadDistribution.cpp:668:44: warning: implicit conversion changes signedness: 'long' to 'size_type' (aka 'unsigned long') [-Wsign-conversion]
if(trLen>singleReadLength*2) effL[m] = trLen - singleReadLength;
˜˜˜˜ ^
ReadDistribution.cpp:669:47: warning: implicit conversion changes signedness: 'long' to 'size_type' (aka 'unsigned long') [-Wsign-conversion]
else if(trLen>singleReadLength) effL[m] = singleReadLength;
˜˜˜˜ ^
ReadDistribution.cpp:670:20: warning: implicit conversion changes signedness: 'long' to 'size_type' (aka 'unsigned long') [-Wsign-conversion]
else effL[m] = trLen;
˜˜˜˜ ^
ReadDistribution.cpp:681:15: warning: implicit conversion changes signedness: 'long' to 'size_type' (aka 'unsigned long') [-Wsign-conversion]
effL[m] = eL>minFragLen?eL:trLen;
˜˜˜˜ ^
ReadDistribution.cpp:683:34: warning: implicit conversion changes signedness: 'long' to 'size_type' (aka 'unsigned long') [-Wsign-conversion]
vector<double> posBias5(trLen),posBias3(trLen);
˜˜˜˜˜˜˜˜ ^˜˜˜˜
ReadDistribution.cpp:683:50: warning: implicit conversion changes signedness: 'long' to 'size_type' (aka 'unsigned long') [-Wsign-conversion]
vector<double> posBias5(trLen),posBias3(trLen);
˜˜˜˜˜˜˜˜ ^˜˜˜˜
ReadDistribution.cpp:685:22: warning: implicit conversion changes signedness: 'long' to 'size_type' (aka 'unsigned long') [-Wsign-conversion]
posBias5[pos] = getPosBias(pos+1, mate_5, m)*getSeqBias(pos+1, mate_5, m);
˜˜˜˜˜˜˜˜ ^˜˜
ReadDistribution.cpp:686:22: warning: implicit conversion changes signedness: 'long' to 'size_type' (aka 'unsigned long') [-Wsign-conversion]
posBias3[pos] = getPosBias(pos, mate_3, m)*getSeqBias(pos, mate_3, m);
˜˜˜˜˜˜˜˜ ^˜˜
ReadDistribution.cpp:693:34: warning: implicit conversion changes signedness: 'long' to 'size_type' (aka 'unsigned long') [-Wsign-conversion]
wNorm += posBias3[pos] * posBias5[pos+len-1];
˜˜˜˜˜˜˜˜ ^˜˜
ReadDistribution.cpp:693:57: warning: implicit conversion changes signedness: 'long' to 'size_type' (aka 'unsigned long') [-Wsign-conversion]
wNorm += posBias3[pos] * posBias5[pos+len-1];
˜˜˜˜˜˜˜˜ ˜˜˜˜˜˜˜^˜
ReadDistribution.cpp:700:15: warning: implicit conversion changes signedness: 'long' to 'size_type' (aka 'unsigned long') [-Wsign-conversion]
effL[m] = eL>minFragLen?eL:trLen;
˜˜˜˜ ^
ReadDistribution.cpp:708:23: warning: implicit conversion changes signedness: 'long' to 'size_type' (aka 'unsigned long') [-Wsign-conversion]
effSum+=effL[m];
˜˜˜˜ ^
ReadDistribution.cpp:710:28: warning: implicit conversion changes signedness: 'long' to 'size_type' (aka 'unsigned long') [-Wsign-conversion]
for(m=0;m<M;m++)effL[m] *= lSum/effSum;
˜˜˜˜ ^
ReadDistribution.cpp:712:28: warning: implicit conversion changes signedness: 'long' to 'size_type' (aka 'unsigned long') [-Wsign-conversion]
for(m=0;m<M;m++)if(effL[m]<=0) effL[m]=1;
˜˜˜˜ ^
ReadDistribution.cpp:712:40: warning: implicit conversion changes signedness: 'long' to 'size_type' (aka 'unsigned long') [-Wsign-conversion]
for(m=0;m<M;m++)if(effL[m]<=0) effL[m]=1;
˜˜˜˜ ^
ReadDistribution.cpp:720:17: warning: implicit conversion changes signedness: 'long' to 'size_type' (aka 'unsigned long') [-Wsign-conversion]
return probs[base2int(b)];
˜˜˜˜˜ ^˜˜˜˜˜˜˜˜˜˜
ReadDistribution.cpp:732:17: warning: implicit conversion changes signedness: 'const long' to 'size_type' (aka 'unsigned long') [-Wsign-conversion]
probs.assign(pows4[parentsN+1], 0.01/pows4[parentsN+1]);
˜˜˜˜˜ ^˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜
ReadDistribution.cpp:750:14: warning: implicit conversion changes signedness: 'long' to 'size_type' (aka 'unsigned long') [-Wsign-conversion]
probs[ i ] += Iexp;
˜˜˜˜˜ ^
ReadDistribution.cpp:761:57: warning: implicit conversion changes signedness: 'long' to 'size_type' (aka 'unsigned long') [-Wsign-conversion]
probs[pows4[2]*i + pows4[1]*j+ k]+=Iexp;
˜˜˜˜˜ ˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜^˜˜
ReadDistribution.cpp:767:38: warning: implicit conversion changes signedness: 'long' to 'size_type' (aka 'unsigned long') [-Wsign-conversion]
probs[pows4[1]*j+ k]+=Iexp;
˜˜˜˜˜ ˜˜˜˜˜˜˜˜˜˜^˜˜
ReadDistribution.cpp:771:22: warning: implicit conversion changes signedness: 'long' to 'size_type' (aka 'unsigned long') [-Wsign-conversion]
probs[k]+=Iexp;
˜˜˜˜˜ ^
ReadDistribution.cpp:783:44: warning: implicit conversion changes signedness: 'long' to 'size_type' (aka 'unsigned long') [-Wsign-conversion]
for(i=0;i<4;i++)sum += probs[i + index];
˜˜˜˜˜ ˜˜^˜˜˜˜˜˜
ReadDistribution.cpp:784:37: warning: implicit conversion changes signedness: 'long' to 'size_type' (aka 'unsigned long') [-Wsign-conversion]
for(i=0;i<4;i++)probs[i + index] /= sum;
˜˜˜˜˜ ˜˜^˜˜˜˜˜˜
ReadDistribution.cpp:790:41: warning: implicit conversion changes signedness: 'long' to 'size_type' (aka 'unsigned long') [-Wsign-conversion]
for(i=0;i<4;i++)sum += probs[i + index];
˜˜˜˜˜ ˜˜^˜˜˜˜˜˜
ReadDistribution.cpp:791:34: warning: implicit conversion changes signedness: 'long' to 'size_type' (aka 'unsigned long') [-Wsign-conversion]
for(i=0;i<4;i++)probs[i + index] /= sum;
˜˜˜˜˜ ˜˜^˜˜˜˜˜˜
ReadDistribution.cpp:795:52: warning: implicit conversion changes signedness: 'long' to 'size_type' (aka 'unsigned long') [-Wsign-conversion]
for(i=0;i<pows4[parentsN+1];i++)sum += probs[i];
˜˜˜˜˜ ^
ReadDistribution.cpp:796:45: warning: implicit conversion changes signedness: 'long' to 'size_type' (aka 'unsigned long') [-Wsign-conversion]
for(i=0;i<pows4[parentsN+1];i++)probs[i] /= sum;
˜˜˜˜˜ ^
ReadDistribution.cpp:815:21: warning: implicit conversion changes signedness: 'long' to 'size_type' (aka 'unsigned long') [-Wsign-conversion]
return probs[ i ];
˜˜˜˜˜ ^
ReadDistribution.cpp:826:59: warning: implicit conversion changes signedness: 'long' to 'size_type' (aka 'unsigned long') [-Wsign-conversion]
prob += probs[pows4[2]*i + pows4[1]*j+ k];
˜˜˜˜˜ ˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜^˜˜
ReadDistribution.cpp:831:37: warning: implicit conversion changes signedness: 'long' to 'size_type' (aka 'unsigned long') [-Wsign-conversion]
prob += probs[pows4[1]*j+ k];
˜˜˜˜˜ ˜˜˜˜˜˜˜˜˜˜^˜˜
139 warnings generated.
clang++ -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -DPACKAGE_NAME=\"Bitseq\" -DPACKAGE_TARNAME=\"bitseq\" -DPACKAGE_VERSION=\"1.4.x\" -DPACKAGE_STRING=\"Bitseq\ 1.4.x\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DBS_VERSION=\"1.4.2\" -DBIOC_BUILD=1 -D_USE_KNETFILE -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -I/usr/local/include -I"/Library/Frameworks/R.framework/Versions/3.0/Resources/library/Rsamtools/include" -I"/Library/Frameworks/R.framework/Versions/3.0/Resources/library/zlibbioc/include" -I. -fPIC -mtune=native -g -O2 -Wall -pedantic -Wconversion -c Sampler.cpp -o Sampler.o
In file included from Sampler.cpp:5:
In file included from ./Sampler.h:6:
In file included from ./boost/random/mersenne_twister.hpp:29:
In file included from ./boost/random/detail/seed_impl.hpp:27:
In file included from ./boost/random/detail/const_mod.hpp:23:
./boost/random/detail/large_arithmetic.hpp:94:14: warning: implicit conversion changes signedness: 'int' to 'unsigned int' [-Wsign-conversion]
q -= error;
˜˜ ^˜˜˜˜
./boost/random/detail/large_arithmetic.hpp:95:21: warning: implicit conversion changes signedness: 'int' to 'unsigned long' [-Wsign-conversion]
rem = rem + error * m - diff;
^˜˜˜˜ ˜
In file included from Sampler.cpp:5:
In file included from ./Sampler.h:6:
./boost/random/mersenne_twister.hpp:493:14: warning: 'long long' is a C++11 extension [-Wc++11-long-long]
UINT64_C(0xb5026f5aa96619e9),29,UINT64_C(0x5555555555555555),17,
^
/usr/include/stdint.h:248:23: note: expanded from macro 'UINT64_C'
#define UINT64_C(v) (v ## ULL)
^
<scratch space>:92:1: note: expanded from macro '0xb5026f5aa96619e9'
0xb5026f5aa96619e9ULL
^
In file included from Sampler.cpp:5:
In file included from ./Sampler.h:6:
./boost/random/mersenne_twister.hpp:493:46: warning: 'long long' is a C++11 extension [-Wc++11-long-long]
UINT64_C(0xb5026f5aa96619e9),29,UINT64_C(0x5555555555555555),17,
^
/usr/include/stdint.h:248:23: note: expanded from macro 'UINT64_C'
#define UINT64_C(v) (v ## ULL)
^
<scratch space>:92:1: note: expanded from macro '0x5555555555555555'
0x5555555555555555ULL
^
In file included from Sampler.cpp:5:
In file included from ./Sampler.h:6:
./boost/random/mersenne_twister.hpp:494:14: warning: 'long long' is a C++11 extension [-Wc++11-long-long]
UINT64_C(0x71d67fffeda60000),37,UINT64_C(0xfff7eee000000000),43,
^
/usr/include/stdint.h:248:23: note: expanded from macro 'UINT64_C'
#define UINT64_C(v) (v ## ULL)
^
<scratch space>:92:1: note: expanded from macro '0x71d67fffeda60000'
0x71d67fffeda60000ULL
^
In file included from Sampler.cpp:5:
In file included from ./Sampler.h:6:
./boost/random/mersenne_twister.hpp:494:46: warning: 'long long' is a C++11 extension [-Wc++11-long-long]
UINT64_C(0x71d67fffeda60000),37,UINT64_C(0xfff7eee000000000),43,
^
/usr/include/stdint.h:248:23: note: expanded from macro 'UINT64_C'
#define UINT64_C(v) (v ## ULL)
^
<scratch space>:92:1: note: expanded from macro '0xfff7eee000000000'
0xfff7eee000000000ULL
^
In file included from Sampler.cpp:5:
In file included from ./Sampler.h:6:
./boost/random/mersenne_twister.hpp:495:14: warning: 'long long' is a C++11 extension [-Wc++11-long-long]
UINT64_C(6364136223846793005)> mt19937_64;
^
/usr/include/stdint.h:248:23: note: expanded from macro 'UINT64_C'
#define UINT64_C(v) (v ## ULL)
^
<scratch space>:92:1: note: expanded from macro '6364136223846793005'
6364136223846793005ULL
^
In file included from Sampler.cpp:6:
./common.h:17:17: warning: variadic macros are a C99 feature [-Wvariadic-macros]
#define message(...) Rprintf(__VA_ARGS__)
^
Sampler.cpp:44:17: warning: implicit conversion changes signedness: 'long' to 'size_type' (aka 'unsigned long') [-Wsign-conversion]
theta.assign(m,0);
˜˜˜˜˜ ^
Sampler.cpp:45:13: warning: implicit conversion changes signedness: 'long' to 'size_type' (aka 'unsigned long') [-Wsign-conversion]
C.assign(m,0);
˜ ^
Sampler.cpp:39:16: warning: implicit conversion loses integer precision: 'long' to 'const unsigned int' [-Wshorten-64-to-32]
rng_mt.seed(seed);
˜˜˜˜˜˜ ^˜˜˜
Sampler.cpp:54:20: warning: implicit conversion changes signedness: 'long' to 'size_type' (aka 'unsigned long') [-Wsign-conversion]
thetaSum.assign(m,pairD(0,0));
˜˜˜˜˜˜˜˜ ^
Sampler.cpp:55:22: warning: implicit conversion changes signedness: 'long' to 'size_type' (aka 'unsigned long') [-Wsign-conversion]
thetaSqSum.assign(m,pairD(0,0));
˜˜˜˜˜˜˜˜˜˜ ^
Sampler.cpp:63:17: warning: implicit conversion changes signedness: 'long' to 'size_type' (aka 'unsigned long') [-Wsign-conversion]
av.assign(m,pairD(0,0));
˜˜ ^
Sampler.cpp:66:13: warning: implicit conversion changes signedness: 'long' to 'size_type' (aka 'unsigned long') [-Wsign-conversion]
av[i].first=thetaSum[i].first/sumNorm.first;
˜˜ ^
Sampler.cpp:66:31: warning: implicit conversion changes signedness: 'long' to 'size_type' (aka 'unsigned long') [-Wsign-conversion]
av[i].first=thetaSum[i].first/sumNorm.first;
˜˜˜˜˜˜˜˜ ^
Sampler.cpp:68:13: warning: implicit conversion changes signedness: 'long' to 'size_type' (aka 'unsigned long') [-Wsign-conversion]
av[i].second=thetaSum[i].second/sumNorm.second;
˜˜ ^
Sampler.cpp:68:32: warning: implicit conversion changes signedness: 'long' to 'size_type' (aka 'unsigned long') [-Wsign-conversion]
av[i].second=thetaSum[i].second/sumNorm.second;
˜˜˜˜˜˜˜˜ ^
Sampler.cpp:73:38: warning: implicit conversion changes signedness: 'long' to 'size_type' (aka 'unsigned long') [-Wsign-conversion]
av1=(sumNorm.first==0)?0:thetaSum[i].first/sumNorm.first;
˜˜˜˜˜˜˜˜ ^
Sampler.cpp:74:39: warning: implicit conversion changes signedness: 'long' to 'size_type' (aka 'unsigned long') [-Wsign-conversion]
av2=(sumNorm.second==0)?0:thetaSum[i].second/sumNorm.second;
˜˜˜˜˜˜˜˜ ^
Sampler.cpp:80:17: warning: implicit conversion changes signedness: 'long' to 'size_type' (aka 'unsigned long') [-Wsign-conversion]
va.assign(m,pairD(0,0));
˜˜ ^
Sampler.cpp:83:13: warning: implicit conversion changes signedness: 'long' to 'size_type' (aka 'unsigned long') [-Wsign-conversion]
va[i].first = thetaSqSum[i].first / sumNorm.first - (thetaSum[i].first/sumNorm.first)*(thetaSum[i].first/sumNorm.first);
˜˜ ^
Sampler.cpp:83:35: warning: implicit conversion changes signedness: 'long' to 'size_type' (aka 'unsigned long') [-Wsign-conversion]
va[i].first = thetaSqSum[i].first / sumNorm.first - (thetaSum[i].first/sumNorm.first)*(thetaSum[i].first/sumNorm.first);
˜˜˜˜˜˜˜˜˜˜ ^
Sampler.cpp:83:72: warning: implicit conversion changes signedness: 'long' to 'size_type' (aka 'unsigned long') [-Wsign-conversion]
va[i].first = thetaSqSum[i].first / sumNorm.first - (thetaSum[i].first/sumNorm.first)*(thetaSum[i].first/sumNorm.first);
˜˜˜˜˜˜˜˜ ^
Sampler.cpp:83:106: warning: implicit conversion changes signedness: 'long' to 'size_type' (aka 'unsigned long') [-Wsign-conversion]
va[i].first = thetaSqSum[i].first / sumNorm.first - (thetaSum[i].first/sumNorm.first)*(thetaSum[i].first/sumNorm.first);
˜˜˜˜˜˜˜˜ ^
Sampler.cpp:85:13: warning: implicit conversion changes signedness: 'long' to 'size_type' (aka 'unsigned long') [-Wsign-conversion]
va[i].second = thetaSqSum[i].first / sumNorm.second - (thetaSum[i].second/sumNorm.second)*(thetaSum[i].second/sumNorm.second);
˜˜ ^
Sampler.cpp:85:36: warning: implicit conversion changes signedness: 'long' to 'size_type' (aka 'unsigned long') [-Wsign-conversion]
va[i].second = thetaSqSum[i].first / sumNorm.second - (thetaSum[i].second/sumNorm.second)*(thetaSum[i].second/sumNorm.second);
˜˜˜˜˜˜˜˜˜˜ ^
Sampler.cpp:85:74: warning: implicit conversion changes signedness: 'long' to 'size_type' (aka 'unsigned long') [-Wsign-conversion]
va[i].second = thetaSqSum[i].first / sumNorm.second - (thetaSum[i].second/sumNorm.second)*(thetaSum[i].second/sumNorm.second);
˜˜˜˜˜˜˜˜ ^
Sampler.cpp:85:110: warning: implicit conversion changes signedness: 'long' to 'size_type' (aka 'unsigned long') [-Wsign-conversion]
va[i].second = thetaSqSum[i].first / sumNorm.second - (thetaSum[i].second/sumNorm.second)*(thetaSum[i].second/sumNorm.second);
˜˜˜˜˜˜˜˜ ^
Sampler.cpp:93:22: warning: implicit conversion changes signedness: 'long' to 'size_type' (aka 'unsigned long') [-Wsign-conversion]
va1=thetaSqSum[i].first/(sumNorm.first-1.0) -
˜˜˜˜˜˜˜˜˜˜ ^
Sampler.cpp:94:22: warning: implicit conversion changes signedness: 'long' to 'size_type' (aka 'unsigned long') [-Wsign-conversion]
(thetaSum[i].first/(sumNorm.first-1.0))*
˜˜˜˜˜˜˜˜ ^
Sampler.cpp:95:22: warning: implicit conversion changes signedness: 'long' to 'size_type' (aka 'unsigned long') [-Wsign-conversion]
(thetaSum[i].first/sumNorm.first);
˜˜˜˜˜˜˜˜ ^
Sampler.cpp:99:22: warning: implicit conversion changes signedness: 'long' to 'size_type' (aka 'unsigned long') [-Wsign-conversion]
va2=thetaSqSum[i].second/(sumNorm.second-1.0) -
˜˜˜˜˜˜˜˜˜˜ ^
Sampler.cpp:100:22: warning: implicit conversion changes signedness: 'long' to 'size_type' (aka 'unsigned long') [-Wsign-conversion]
(thetaSum[i].second/(sumNorm.second-1.0))*
˜˜˜˜˜˜˜˜ ^
Sampler.cpp:101:22: warning: implicit conversion changes signedness: 'long' to 'size_type' (aka 'unsigned long') [-Wsign-conversion]
(thetaSum[i].second/sumNorm.second);
˜˜˜˜˜˜˜˜ ^
Sampler.cpp:102:54: warning: implicit conversion changes signedness: 'long' to 'size_type' (aka 'unsigned long') [-Wsign-conversion]
if(va1<0)message("minus %lg %lg %lg\n",thetaSqSum[i].first,thetaSum[i].first,sumNorm.first);
˜˜˜˜˜˜˜˜˜˜ ^
./common.h:17:30: note: expanded from macro 'message'
#define message(...) Rprintf(__VA_ARGS__)
^
Sampler.cpp:102:72: warning: implicit conversion changes signedness: 'long' to 'size_type' (aka 'unsigned long') [-Wsign-conversion]
if(va1<0)message("minus %lg %lg %lg\n",thetaSqSum[i].first,thetaSum[i].first,sumNorm.first);
˜˜˜˜˜˜˜˜ ^
./common.h:17:30: note: expanded from macro 'message'
#define message(...) Rprintf(__VA_ARGS__)
^
Sampler.cpp:112:15: warning: implicit conversion changes signedness: 'long' to 'size_type' (aka 'unsigned long') [-Wsign-conversion]
tau.assign(Sof(tau),0);
˜˜˜ ^˜˜˜˜˜˜˜
Sampler.cpp:8:16: note: expanded from macro 'Sof'
#define Sof(x) (long)x.size()
^˜˜˜˜˜˜˜˜˜˜˜˜˜
Sampler.cpp:117:12: warning: implicit conversion changes signedness: 'long' to 'size_type' (aka 'unsigned long') [-Wsign-conversion]
tau[ i ] = theta[i] / (*isoformLengths)[ i ] * norm;
˜˜˜ ^
Sampler.cpp:117:24: warning: implicit conversion changes signedness: 'long' to 'size_type' (aka 'unsigned long') [-Wsign-conversion]
tau[ i ] = theta[i] / (*isoformLengths)[ i ] * norm;
˜˜˜˜˜ ^
Sampler.cpp:117:48: warning: implicit conversion changes signedness: 'long' to 'size_type' (aka 'unsigned long') [-Wsign-conversion]
tau[ i ] = theta[i] / (*isoformLengths)[ i ] * norm;
˜ ^
Sampler.cpp:118:21: warning: implicit conversion changes signedness: 'long' to 'size_type' (aka 'unsigned long') [-Wsign-conversion]
tauSum += tau[i];
˜˜˜ ^
Sampler.cpp:122:14: warning: implicit conversion changes signedness: 'long' to 'size_type' (aka 'unsigned long') [-Wsign-conversion]
if(tau[i]>0) tau[i] /= tauSum;
˜˜˜ ^
Sampler.cpp:122:24: warning: implicit conversion changes signedness: 'long' to 'size_type' (aka 'unsigned long') [-Wsign-conversion]
if(tau[i]>0) tau[i] /= tauSum;
˜˜˜ ^
Sampler.cpp:135:31: warning: implicit conversion changes signedness: 'long' to 'size_type' (aka 'unsigned long') [-Wsign-conversion]
(*outFile)<<theta[i]*norm<<" ";
˜˜˜˜˜ ^
Sampler.cpp:141:34: warning: implicit conversion changes signedness: 'long' to 'size_type' (aka 'unsigned long') [-Wsign-conversion]
if((*isoformLengths)[i]>0)
˜ ^
Sampler.cpp:142:34: warning: implicit conversion changes signedness: 'long' to 'size_type' (aka 'unsigned long') [-Wsign-conversion]
(*outFile)<<theta[i]*norm/(*isoformLengths)[i]<<" ";
˜˜˜˜˜ ^
Sampler.cpp:142:60: warning: implicit conversion changes signedness: 'long' to 'size_type' (aka 'unsigned long') [-Wsign-conversion]
(*outFile)<<theta[i]*norm/(*isoformLengths)[i]<<" ";
˜ ^
Sampler.cpp:144:34: warning: implicit conversion changes signedness: 'long' to 'size_type' (aka 'unsigned long') [-Wsign-conversion]
(*outFile)<<theta[i]*norm<<" ";
˜˜˜˜˜ ^
Sampler.cpp:150:31: warning: implicit conversion changes signedness: 'long' to 'size_type' (aka 'unsigned long') [-Wsign-conversion]
(*outFile)<<theta[i]*norm<<" ";
˜˜˜˜˜ ^
Sampler.cpp:155:29: warning: implicit conversion changes signedness: 'long' to 'size_type' (aka 'unsigned long') [-Wsign-conversion]
vector<double> tau(m);
˜˜˜ ^
Sampler.cpp:158:29: warning: implicit conversion changes signedness: 'long' to 'size_type' (aka 'unsigned long') [-Wsign-conversion]
(*outFile)<<tau[i]<<" ";
˜˜˜ ^
Sampler.cpp:166:16: warning: implicit conversion changes signedness: 'long' to 'size_type' (aka 'unsigned long') [-Wsign-conversion]
thetaSum[i].first+=theta[i];
˜˜˜˜˜˜˜˜ ^
Sampler.cpp:166:32: warning: implicit conversion changes signedness: 'long' to 'size_type' (aka 'unsigned long') [-Wsign-conversion]
thetaSum[i].first+=theta[i];
˜˜˜˜˜ ^
Sampler.cpp:167:18: warning: implicit conversion changes signedness: 'long' to 'size_type' (aka 'unsigned long') [-Wsign-conversion]
thetaSqSum[i].first+=theta[i]*theta[i];
˜˜˜˜˜˜˜˜˜˜ ^
Sampler.cpp:167:34: warning: implicit conversion changes signedness: 'long' to 'size_type' (aka 'unsigned long') [-Wsign-conversion]
thetaSqSum[i].first+=theta[i]*theta[i];
˜˜˜˜˜ ^
Sampler.cpp:167:43: warning: implicit conversion changes signedness: 'long' to 'size_type' (aka 'unsigned long') [-Wsign-conversion]
thetaSqSum[i].first+=theta[i]*theta[i];
˜˜˜˜˜ ^
Sampler.cpp:173:19: warning: implicit conversion changes signedness: 'long' to 'size_type' (aka 'unsigned long') [-Wsign-conversion]
thetaSum[i].second+=theta[i];
˜˜˜˜˜˜˜˜ ^
Sampler.cpp:173:36: warning: implicit conversion changes signedness: 'long' to 'size_type' (aka 'unsigned long') [-Wsign-conversion]
thetaSum[i].second+=theta[i];
˜˜˜˜˜ ^
Sampler.cpp:174:21: warning: implicit conversion changes signedness: 'long' to 'size_type' (aka 'unsigned long') [-Wsign-conversion]
thetaSqSum[i].second+=theta[i]*theta[i];
˜˜˜˜˜˜˜˜˜˜ ^
Sampler.cpp:174:38: warning: implicit conversion changes signedness: 'long' to 'size_type' (aka 'unsigned long') [-Wsign-conversion]
thetaSqSum[i].second+=theta[i]*theta[i];
˜˜˜˜˜ ^
Sampler.cpp:174:47: warning: implicit conversion changes signedness: 'long' to 'size_type' (aka 'unsigned long') [-Wsign-conversion]
thetaSqSum[i].second+=theta[i]*theta[i];
˜˜˜˜˜ ^
Sampler.cpp:202:25: warning: implicit conversion changes signedness: 'long' to 'size_type' (aka 'unsigned long') [-Wsign-conversion]
vector<double> gamma(m,0);
˜˜˜˜˜ ^
Sampler.cpp:206:50: warning: implicit conversion changes signedness: 'long' to 'size_type' (aka 'unsigned long') [-Wsign-conversion]
gammaDistribution.param(gDP(dir->alpha + C[i], dir->beta));
˜ ^
Sampler.cpp:207:13: warning: implicit conversion changes signedness: 'long' to 'size_type' (aka 'unsigned long') [-Wsign-conversion]
gamma[i]=gammaDistribution(rng_mt);
˜˜˜˜˜ ^
Sampler.cpp:208:23: warning: implicit conversion changes signedness: 'long' to 'size_type' (aka 'unsigned long') [-Wsign-conversion]
gammaSum+=gamma[i];
˜˜˜˜˜ ^
Sampler.cpp:214:13: warning: implicit conversion changes signedness: 'long' to 'size_type' (aka 'unsigned long') [-Wsign-conversion]
theta[i]=gamma[i]/gammaSum;
˜˜˜˜˜ ^
Sampler.cpp:214:22: warning: implicit conversion changes signedness: 'long' to 'size_type' (aka 'unsigned long') [-Wsign-conversion]
theta[i]=gamma[i]/gammaSum;
˜˜˜˜˜ ^
68 warnings generated.
clang++ -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -DPACKAGE_NAME=\"Bitseq\" -DPACKAGE_TARNAME=\"bitseq\" -DPACKAGE_VERSION=\"1.4.x\" -DPACKAGE_STRING=\"Bitseq\ 1.4.x\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DBS_VERSION=\"1.4.2\" -DBIOC_BUILD=1 -D_USE_KNETFILE -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -I/usr/local/include -I"/Library/Frameworks/R.framework/Versions/3.0/Resources/library/Rsamtools/include" -I"/Library/Frameworks/R.framework/Versions/3.0/Resources/library/zlibbioc/include" -I. -fPIC -mtune=native -g -O2 -Wall -pedantic -Wconversion -c TagAlignments.cpp -o TagAlignments.o
In file included from TagAlignments.cpp:5:
./common.h:17:17: warning: variadic macros are a C99 feature [-Wvariadic-macros]
#define message(...) Rprintf(__VA_ARGS__)
^
TagAlignments.cpp:23:31: warning: implicit conversion changes signedness: 'long' to 'size_type' (aka 'unsigned long') [-Wsign-conversion]
readIndex.reserve(Nreads+2);
˜˜˜˜˜˜˜˜˜ ˜˜˜˜˜˜^˜
TagAlignments.cpp:31:21: warning: implicit conversion changes signedness: 'long' to 'size_type' (aka 'unsigned long') [-Wsign-conversion]
trIds.reserve(reservedN);
˜˜˜˜˜ ^˜˜˜˜˜˜˜˜
TagAlignments.cpp:32:21: warning: implicit conversion changes signedness: 'long' to 'size_type' (aka 'unsigned long') [-Wsign-conversion]
probs.reserve(reservedN);
˜˜˜˜˜ ^˜˜˜˜˜˜˜˜
TagAlignments.cpp:36:29: warning: implicit conversion changes signedness: 'long' to 'size_type' (aka 'unsigned long') [-Wsign-conversion]
readsInIsoform.assign(M,-1);
˜˜˜˜˜˜˜˜˜˜˜˜˜˜ ^
TagAlignments.cpp:48:29: warning: implicit conversion changes signedness: 'long' to 'size_type' (aka 'unsigned long') [-Wsign-conversion]
readsInIsoform.resize(M,-1);
˜˜˜˜˜˜˜˜˜˜˜˜˜˜ ^
TagAlignments.cpp:50:22: warning: implicit conversion changes signedness: 'long' to 'size_type' (aka 'unsigned long') [-Wsign-conversion]
if(readsInIsoform[trId] == currentRead){
˜˜˜˜˜˜˜˜˜˜˜˜˜˜ ^˜˜˜
TagAlignments.cpp:52:27: warning: implicit conversion changes signedness: 'long' to 'size_type' (aka 'unsigned long') [-Wsign-conversion]
for(long i=readIndex[currentRead];i<(long)trIds.size();i++)
˜˜˜˜˜˜˜˜˜ ^˜˜˜˜˜˜˜˜˜˜
TagAlignments.cpp:53:18: warning: implicit conversion changes signedness: 'long' to 'size_type' (aka 'unsigned long') [-Wsign-conversion]
if(trIds[i] == trId){
˜˜˜˜˜ ^
TagAlignments.cpp:54:18: warning: implicit conversion changes signedness: 'long' to 'size_type' (aka 'unsigned long') [-Wsign-conversion]
probs[i] = ns_math::logAddExp(probs[i], lProb);
˜˜˜˜˜ ^
TagAlignments.cpp:54:48: warning: implicit conversion changes signedness: 'long' to 'size_type' (aka 'unsigned long') [-Wsign-conversion]
probs[i] = ns_math::logAddExp(probs[i], lProb);
˜˜˜˜˜ ^
TagAlignments.cpp:68:27: warning: implicit conversion changes signedness: 'long' to 'size_type' (aka 'unsigned long') [-Wsign-conversion]
trIds.reserve(reservedN);
˜˜˜˜˜ ^˜˜˜˜˜˜˜˜
TagAlignments.cpp:69:27: warning: implicit conversion changes signedness: 'long' to 'size_type' (aka 'unsigned long') [-Wsign-conversion]
probs.reserve(reservedN);
˜˜˜˜˜ ^˜˜˜˜˜˜˜˜
TagAlignments.cpp:81:27: warning: implicit conversion changes signedness: 'long' to 'size_type' (aka 'unsigned long') [-Wsign-conversion]
trIds.reserve(reservedN);
˜˜˜˜˜ ^˜˜˜˜˜˜˜˜
TagAlignments.cpp:82:27: warning: implicit conversion changes signedness: 'long' to 'size_type' (aka 'unsigned long') [-Wsign-conversion]
probs.reserve(reservedN);
˜˜˜˜˜ ^˜˜˜˜˜˜˜˜
TagAlignments.cpp:91:22: warning: implicit conversion changes signedness: 'long' to 'size_type' (aka 'unsigned long') [-Wsign-conversion]
readsInIsoform[trId] = currentRead;
˜˜˜˜˜˜˜˜˜˜˜˜˜˜ ^˜˜˜
TagAlignments.cpp:88:23: warning: implicit conversion loses integer precision: 'long' to 'const value_type' (aka 'const int') [-Wshorten-64-to-32]
trIds.push_back(trId);
˜˜˜˜˜ ^˜˜˜
TagAlignments.cpp:91:30: warning: implicit conversion loses integer precision: 'long' to 'int' [-Wshorten-64-to-32]
readsInIsoform[trId] = currentRead;
˜ ^˜˜˜˜˜˜˜˜˜˜
TagAlignments.cpp:96:17: warning: implicit conversion changes signedness: 'long' to 'size_type' (aka 'unsigned long') [-Wsign-conversion]
if(readIndex[currentRead] == (int_least32_t) probs.size()){
˜˜˜˜˜˜˜˜˜ ^˜˜˜˜˜˜˜˜˜˜
TagAlignments.cpp:102:59: warning: implicit conversion changes signedness: 'long' to 'size_type' (aka 'unsigned long') [-Wsign-conversion]
double logSum = ns_math::logSumExp(probs, readIndex[currentRead], probs.size());
˜˜˜˜˜˜˜˜˜ ^˜˜˜˜˜˜˜˜˜˜
TagAlignments.cpp:102:73: warning: implicit conversion changes signedness: 'size_type' (aka 'unsigned long') to 'long' [-Wsign-conversion]
double logSum = ns_math::logSumExp(probs, readIndex[currentRead], probs.size());
˜˜˜˜˜˜˜ ^˜˜˜˜˜˜˜˜˜˜˜
TagAlignments.cpp:103:30: warning: implicit conversion changes signedness: 'long' to 'size_type' (aka 'unsigned long') [-Wsign-conversion]
for(long i = readIndex[currentRead]; i<(long)probs.size(); i++)
˜˜˜˜˜˜˜˜˜ ^˜˜˜˜˜˜˜˜˜˜
TagAlignments.cpp:104:16: warning: implicit conversion changes signedness: 'long' to 'size_type' (aka 'unsigned long') [-Wsign-conversion]
probs[i] = exp(probs[i]-logSum);
˜˜˜˜˜ ^
TagAlignments.cpp:104:31: warning: implicit conversion changes signedness: 'long' to 'size_type' (aka 'unsigned long') [-Wsign-conversion]
probs[i] = exp(probs[i]-logSum);
˜˜˜˜˜ ^
TagAlignments.cpp:108:24: warning: implicit conversion loses integer precision: 'size_type' (aka 'unsigned long') to 'const value_type' (aka 'const int') [-Wshorten-64-to-32]
readIndex.push_back(probs.size());
˜˜˜˜˜˜˜˜˜ ^˜˜˜˜˜˜˜˜˜˜˜
TagAlignments.cpp:111:19: warning: implicit conversion changes signedness: 'size_type' (aka 'unsigned long') to 'long' [-Wsign-conversion]
*M = this->M = readsInIsoform.size();
˜ ^˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜
TagAlignments.cpp:112:46: warning: implicit conversion changes signedness: 'unsigned long' to 'long' [-Wsign-conversion]
*Nreads = this->Nreads = readIndex.size() - 1;
˜ ˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜^˜˜
TagAlignments.cpp:113:29: warning: implicit conversion changes signedness: 'size_type' (aka 'unsigned long') to 'long' [-Wsign-conversion]
*Ntotal = this->Ntotal = probs.size();
˜ ^˜˜˜˜˜˜˜˜˜˜˜
TagAlignments.cpp:120:29: warning: implicit conversion changes signedness: 'long' to 'size_type' (aka 'unsigned long') [-Wsign-conversion]
if(i<Ntotal)return trIds[i];
˜˜˜˜˜ ^
TagAlignments.cpp:124:29: warning: implicit conversion changes signedness: 'long' to 'size_type' (aka 'unsigned long') [-Wsign-conversion]
if(i<Ntotal)return probs[i];
˜˜˜˜˜ ^
TagAlignments.cpp:128:34: warning: implicit conversion changes signedness: 'long' to 'size_type' (aka 'unsigned long') [-Wsign-conversion]
if(i<=Nreads)return readIndex[i];
˜˜˜˜˜˜˜˜˜ ^
31 warnings generated.
clang++ -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -DPACKAGE_NAME=\"Bitseq\" -DPACKAGE_TARNAME=\"bitseq\" -DPACKAGE_VERSION=\"1.4.x\" -DPACKAGE_STRING=\"Bitseq\ 1.4.x\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DBS_VERSION=\"1.4.2\" -DBIOC_BUILD=1 -D_USE_KNETFILE -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -I/usr/local/include -I"/Library/Frameworks/R.framework/Versions/3.0/Resources/library/Rsamtools/include" -I"/Library/Frameworks/R.framework/Versions/3.0/Resources/library/zlibbioc/include" -I. -fPIC -mtune=native -g -O2 -Wall -pedantic -Wconversion -c TranscriptExpression.cpp -o TranscriptExpression.o
In file included from TranscriptExpression.cpp:3:
./TranscriptExpression.h:32:38: warning: implicit conversion changes signedness: 'long' to 'size_type' (aka 'unsigned long') [-Wsign-conversion]
double exp(long tr){return trs[tr].exp;}
˜˜˜ ^˜
./TranscriptExpression.h:33:38: warning: implicit conversion changes signedness: 'long' to 'size_type' (aka 'unsigned long') [-Wsign-conversion]
double var(long tr){return trs[tr].var;}
˜˜˜ ^˜
./TranscriptExpression.h:34:35: warning: implicit conversion changes signedness: 'long' to 'size_type' (aka 'unsigned long') [-Wsign-conversion]
long id(long tr){return trs[tr].id;}
˜˜˜ ^˜
In file included from TranscriptExpression.cpp:5:
./common.h:17:17: warning: variadic macros are a C99 feature [-Wvariadic-macros]
#define message(...) Rprintf(__VA_ARGS__)
^
TranscriptExpression.cpp:23:15: warning: implicit conversion changes signedness: 'long' to 'size_type' (aka 'unsigned long') [-Wsign-conversion]
trs.resize(M);
˜˜˜ ^
TranscriptExpression.cpp:26:14: warning: implicit conversion changes signedness: 'long' to 'size_type' (aka 'unsigned long') [-Wsign-conversion]
trs[i].var=0;
˜˜˜ ^
TranscriptExpression.cpp:27:23: warning: implicit conversion changes signedness: 'long' to 'size_type' (aka 'unsigned long') [-Wsign-conversion]
varFile>>trs[i].id>>trs[i].exp;
˜˜˜ ^
TranscriptExpression.cpp:27:34: warning: implicit conversion changes signedness: 'long' to 'size_type' (aka 'unsigned long') [-Wsign-conversion]
varFile>>trs[i].id>>trs[i].exp;
˜˜˜ ^
TranscriptExpression.cpp:29:14: warning: implicit conversion changes signedness: 'long' to 'size_type' (aka 'unsigned long') [-Wsign-conversion]
trs[i].id--;
˜˜˜ ^
TranscriptExpression.cpp:38:14: warning: implicit conversion changes signedness: 'long' to 'size_type' (aka 'unsigned long') [-Wsign-conversion]
trs[i].id=i;
˜˜˜ ^
TranscriptExpression.cpp:39:23: warning: implicit conversion changes signedness: 'long' to 'size_type' (aka 'unsigned long') [-Wsign-conversion]
varFile>>trs[i].exp>>trs[i].var;
˜˜˜ ^
TranscriptExpression.cpp:39:35: warning: implicit conversion changes signedness: 'long' to 'size_type' (aka 'unsigned long') [-Wsign-conversion]
varFile>>trs[i].exp>>trs[i].var;
˜˜˜ ^
TranscriptExpression.cpp:38:20: warning: implicit conversion loses integer precision: 'long' to 'int_least32_t' (aka 'int') [-Wshorten-64-to-32]
trs[i].id=i;
˜^
13 warnings generated.
clang++ -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -DPACKAGE_NAME=\"Bitseq\" -DPACKAGE_TARNAME=\"bitseq\" -DPACKAGE_VERSION=\"1.4.x\" -DPACKAGE_STRING=\"Bitseq\ 1.4.x\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DBS_VERSION=\"1.4.2\" -DBIOC_BUILD=1 -D_USE_KNETFILE -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -I/usr/local/include -I"/Library/Frameworks/R.framework/Versions/3.0/Resources/library/Rsamtools/include" -I"/Library/Frameworks/R.framework/Versions/3.0/Resources/library/zlibbioc/include" -I. -fPIC -mtune=native -g -O2 -Wall -pedantic -Wconversion -c TranscriptInfo.cpp -o TranscriptInfo.o
In file included from TranscriptInfo.cpp:3:
./common.h:17:17: warning: variadic macros are a C99 feature [-Wvariadic-macros]
#define message(...) Rprintf(__VA_ARGS__)
^
TranscriptInfo.cpp:20:24: warning: implicit conversion changes signedness: 'long' to 'size_type' (aka 'unsigned long') [-Wsign-conversion]
trF<<transcripts[i].g<<" "<<transcripts[i].t<<" "<<transcripts[i].l<<" "<<transcripts[i].effL<<endl;
˜˜˜˜˜˜˜˜˜˜˜ ^
TranscriptInfo.cpp:20:47: warning: implicit conversion changes signedness: 'long' to 'size_type' (aka 'unsigned long') [-Wsign-conversion]
trF<<transcripts[i].g<<" "<<transcripts[i].t<<" "<<transcripts[i].l<<" "<<transcripts[i].effL<<endl;
˜˜˜˜˜˜˜˜˜˜˜ ^
TranscriptInfo.cpp:20:70: warning: implicit conversion changes signedness: 'long' to 'size_type' (aka 'unsigned long') [-Wsign-conversion]
trF<<transcripts[i].g<<" "<<transcripts[i].t<<" "<<transcripts[i].l<<" "<<transcripts[i].effL<<endl;
˜˜˜˜˜˜˜˜˜˜˜ ^
TranscriptInfo.cpp:20:93: warning: implicit conversion changes signedness: 'long' to 'size_type' (aka 'unsigned long') [-Wsign-conversion]
trF<<transcripts[i].g<<" "<<transcripts[i].t<<" "<<transcripts[i].l<<" "<<transcripts[i].effL<<endl;
˜˜˜˜˜˜˜˜˜˜˜ ^
TranscriptInfo.cpp:31:21: warning: implicit conversion changes signedness: 'long' to 'size_type' (aka 'unsigned long') [-Wsign-conversion]
newT.g=gNames[i];
˜˜˜˜˜˜ ^
TranscriptInfo.cpp:32:21: warning: implicit conversion changes signedness: 'long' to 'size_type' (aka 'unsigned long') [-Wsign-conversion]
newT.t=tNames[i];
˜˜˜˜˜˜ ^
TranscriptInfo.cpp:33:37: warning: implicit conversion changes signedness: 'long' to 'size_type' (aka 'unsigned long') [-Wsign-conversion]
newT.l=(int_least32_t)lengths[i];
˜˜˜˜˜˜˜ ^
TranscriptInfo.cpp:34:27: warning: implicit conversion changes signedness: 'long' to 'size_type' (aka 'unsigned long') [-Wsign-conversion]
newT.effL = lengths[i];
˜˜˜˜˜˜˜ ^
TranscriptInfo.cpp:51:22: warning: implicit conversion changes signedness: 'long' to 'size_type' (aka 'unsigned long') [-Wsign-conversion]
if(transcripts[i].g == previousName){
˜˜˜˜˜˜˜˜˜˜˜ ^
TranscriptInfo.cpp:52:16: warning: implicit conversion changes signedness: 'long' to 'size_type' (aka 'unsigned long') [-Wsign-conversion]
genes[gi].m++;
˜˜˜˜˜ ^˜
TranscriptInfo.cpp:53:16: warning: implicit conversion changes signedness: 'long' to 'size_type' (aka 'unsigned long') [-Wsign-conversion]
genes[gi].trs.push_back(i);
˜˜˜˜˜ ^˜
TranscriptInfo.cpp:56:37: warning: implicit conversion changes signedness: 'long' to 'size_type' (aka 'unsigned long') [-Wsign-conversion]
if(names.count(transcripts[i].g) == 0){
˜˜˜˜˜˜˜˜˜˜˜ ^
TranscriptInfo.cpp:58:37: warning: implicit conversion changes signedness: 'long' to 'size_type' (aka 'unsigned long') [-Wsign-conversion]
tmpG.name = transcripts[i].g;
˜˜˜˜˜˜˜˜˜˜˜ ^
TranscriptInfo.cpp:64:28: warning: implicit conversion changes signedness: 'unsigned long' to 'long' [-Wsign-conversion]
gi=genes.size()-1;
˜˜˜˜˜˜˜˜˜˜˜˜˜^˜
TranscriptInfo.cpp:66:31: warning: implicit conversion changes signedness: 'long' to 'size_type' (aka 'unsigned long') [-Wsign-conversion]
names[transcripts[i].g] = gi;
˜˜˜˜˜˜˜˜˜˜˜ ^
TranscriptInfo.cpp:67:38: warning: implicit conversion changes signedness: 'long' to 'size_type' (aka 'unsigned long') [-Wsign-conversion]
previousName=transcripts[i].g;
˜˜˜˜˜˜˜˜˜˜˜ ^
TranscriptInfo.cpp:72:36: warning: implicit conversion changes signedness: 'long' to 'size_type' (aka 'unsigned long') [-Wsign-conversion]
gi = names[transcripts[i].g];
˜˜˜˜˜˜˜˜˜˜˜ ^
TranscriptInfo.cpp:73:19: warning: implicit conversion changes signedness: 'long' to 'size_type' (aka 'unsigned long') [-Wsign-conversion]
genes[gi].m++;
˜˜˜˜˜ ^˜
TranscriptInfo.cpp:74:19: warning: implicit conversion changes signedness: 'long' to 'size_type' (aka 'unsigned long') [-Wsign-conversion]
genes[gi].trs.push_back(i);
˜˜˜˜˜ ^˜
TranscriptInfo.cpp:78:8: warning: implicit conversion changes signedness: 'size_type' (aka 'unsigned long') to 'long' [-Wsign-conversion]
G = genes.size();
˜ ^˜˜˜˜˜˜˜˜˜˜˜
TranscriptInfo.cpp:134:18: warning: implicit conversion changes signedness: 'long' to 'size_type' (aka 'unsigned long') [-Wsign-conversion]
return &genes[i].trs;
˜˜˜˜˜ ^
TranscriptInfo.cpp:137:49: warning: implicit conversion changes signedness: 'long' to 'size_type' (aka 'unsigned long') [-Wsign-conversion]
if(isInitialized && (i<M))return transcripts[i].effL;
˜˜˜˜˜˜˜˜˜˜˜ ^
TranscriptInfo.cpp:141:49: warning: implicit conversion changes signedness: 'long' to 'size_type' (aka 'unsigned long') [-Wsign-conversion]
if(isInitialized && (i<M))return transcripts[i].l;
˜˜˜˜˜˜˜˜˜˜˜ ^
TranscriptInfo.cpp:145:49: warning: implicit conversion changes signedness: 'long' to 'size_type' (aka 'unsigned long') [-Wsign-conversion]
if(isInitialized && (i<M))return transcripts[i].t;
˜˜˜˜˜˜˜˜˜˜˜ ^
TranscriptInfo.cpp:149:49: warning: implicit conversion changes signedness: 'long' to 'size_type' (aka 'unsigned long') [-Wsign-conversion]
if(isInitialized && (i<M))return transcripts[i].g;
˜˜˜˜˜˜˜˜˜˜˜ ^
TranscriptInfo.cpp:160:18: warning: implicit conversion changes signedness: 'long' to 'size_type' (aka 'unsigned long') [-Wsign-conversion]
sumN+=effL[i];
˜˜˜˜ ^
TranscriptInfo.cpp:161:25: warning: implicit conversion changes signedness: 'long' to 'size_type' (aka 'unsigned long') [-Wsign-conversion]
sumL+=transcripts[i].l;
˜˜˜˜˜˜˜˜˜˜˜ ^
TranscriptInfo.cpp:167:19: warning: implicit conversion changes signedness: 'long' to 'size_type' (aka 'unsigned long') [-Wsign-conversion]
transcripts[i].effL = effL[i] * norm;
˜˜˜˜˜˜˜˜˜˜˜ ^
TranscriptInfo.cpp:167:34: warning: implicit conversion changes signedness: 'long' to 'size_type' (aka 'unsigned long') [-Wsign-conversion]
transcripts[i].effL = effL[i] * norm;
˜˜˜˜ ^
TranscriptInfo.cpp:171:45: warning: implicit conversion changes signedness: 'long' to 'size_type' (aka 'unsigned long') [-Wsign-conversion]
vector<double> *Ls = new vector<double>(M+1);
˜˜˜˜˜˜ ˜^˜
TranscriptInfo.cpp:173:27: warning: implicit conversion changes signedness: 'long' to 'size_type' (aka 'unsigned long') [-Wsign-conversion]
if(effective)(*Ls)[i+1] = transcripts[i].effL;
˜ ˜^˜
TranscriptInfo.cpp:173:45: warning: implicit conversion changes signedness: 'long' to 'size_type' (aka 'unsigned long') [-Wsign-conversion]
if(effective)(*Ls)[i+1] = transcripts[i].effL;
˜˜˜˜˜˜˜˜˜˜˜ ^
TranscriptInfo.cpp:174:19: warning: implicit conversion changes signedness: 'long' to 'size_type' (aka 'unsigned long') [-Wsign-conversion]
else (*Ls)[i+1] = transcripts[i].l;
˜ ˜^˜
TranscriptInfo.cpp:174:37: warning: implicit conversion changes signedness: 'long' to 'size_type' (aka 'unsigned long') [-Wsign-conversion]
else (*Ls)[i+1] = transcripts[i].l;
˜˜˜˜˜˜˜˜˜˜˜ ^
TranscriptInfo.cpp:185:19: warning: implicit conversion changes signedness: 'long' to 'size_type' (aka 'unsigned long') [-Wsign-conversion]
transcripts[i].g = geneList[i];
˜˜˜˜˜˜˜˜˜˜˜ ^
TranscriptInfo.cpp:185:35: warning: implicit conversion changes signedness: 'long' to 'size_type' (aka 'unsigned long') [-Wsign-conversion]
transcripts[i].g = geneList[i];
˜˜˜˜˜˜˜˜ ^
TranscriptInfo.cpp:198:40: warning: implicit conversion changes signedness: 'long' to 'size_type' (aka 'unsigned long') [-Wsign-conversion]
if(!trGeneList.count(transcripts[i].t)){
˜˜˜˜˜˜˜˜˜˜˜ ^
TranscriptInfo.cpp:199:82: warning: implicit conversion changes signedness: 'long' to 'size_type' (aka 'unsigned long') [-Wsign-conversion]
warning("TranscriptInfo: No gene name for transcript [%s].",transcripts[i].t.c_str());
˜˜˜˜˜˜˜˜˜˜˜ ^
TranscriptInfo.cpp:205:19: warning: implicit conversion changes signedness: 'long' to 'size_type' (aka 'unsigned long') [-Wsign-conversion]
transcripts[i].g = trGeneList.find(transcripts[i].t)->second;
˜˜˜˜˜˜˜˜˜˜˜ ^
TranscriptInfo.cpp:205:54: warning: implicit conversion changes signedness: 'long' to 'size_type' (aka 'unsigned long') [-Wsign-conversion]
transcripts[i].g = trGeneList.find(transcripts[i].t)->second;
˜˜˜˜˜˜˜˜˜˜˜ ^
41 warnings generated.
clang++ -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -DPACKAGE_NAME=\"Bitseq\" -DPACKAGE_TARNAME=\"bitseq\" -DPACKAGE_VERSION=\"1.4.x\" -DPACKAGE_STRING=\"Bitseq\ 1.4.x\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DBS_VERSION=\"1.4.2\" -DBIOC_BUILD=1 -D_USE_KNETFILE -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -I/usr/local/include -I"/Library/Frameworks/R.framework/Versions/3.0/Resources/library/Rsamtools/include" -I"/Library/Frameworks/R.framework/Versions/3.0/Resources/library/zlibbioc/include" -I. -fPIC -mtune=native -g -O2 -Wall -pedantic -Wconversion -c TranscriptSequence.cpp -o TranscriptSequence.o
In file included from TranscriptSequence.cpp:6:
./TranscriptSequence.h:55:27: warning: implicit conversion changes signedness: 'size_type' (aka 'unsigned long') to 'long' [-Wsign-conversion]
long getG(){ return geneNames.size(); }
˜˜˜˜˜˜ ^˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜
In file included from TranscriptSequence.cpp:8:
./common.h:17:17: warning: variadic macros are a C99 feature [-Wvariadic-macros]
#define message(...) Rprintf(__VA_ARGS__)
^
TranscriptSequence.cpp:14:10: warning: implicit conversion loses integer precision: 'time_t' (aka 'long') to 'unsigned int' [-Wshorten-64-to-32]
srand(time(NULL));
˜˜˜˜˜ ^˜˜˜˜˜˜˜˜˜
TranscriptSequence.cpp:44:11: warning: implicit conversion changes signedness: 'const unsigned long' to 'long' [-Wsign-conversion]
pos=min(trDesc.find("gene:"),trDesc.find("gene="));
˜^˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜
TranscriptSequence.cpp:47:40: warning: implicit conversion changes signedness: 'long' to 'size_type' (aka 'unsigned long') [-Wsign-conversion]
geneDesc.str(trDesc.substr(pos+5));
˜˜˜˜˜˜ ˜˜˜^˜
TranscriptSequence.cpp:62:8: warning: implicit conversion changes signedness: 'size_type' (aka 'unsigned long') to 'long' [-Wsign-conversion]
M = trs.size();
˜ ^˜˜˜˜˜˜˜˜˜
TranscriptSequence.cpp:64:17: warning: implicit conversion changes signedness: 'const long' to 'size_type' (aka 'unsigned long') [-Wsign-conversion]
cache.resize(min(M,(long)TRS_CACHE_MAX));
˜˜˜˜˜ ^˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜
TranscriptSequence.cpp:65:21: warning: implicit conversion changes signedness: 'const long' to 'size_type' (aka 'unsigned long') [-Wsign-conversion]
cachedTrs.resize(min(M,(long)TRS_CACHE_MAX));
˜˜˜˜˜˜˜˜˜ ^˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜
TranscriptSequence.cpp:73:8: warning: implicit conversion changes signedness: 'long' to 'size_type' (aka 'unsigned long') [-Wsign-conversion]
trs[tr].lastUse = useCounter++;
˜˜˜ ^˜
TranscriptSequence.cpp:75:18: warning: implicit conversion changes signedness: 'long' to 'size_type' (aka 'unsigned long') [-Wsign-conversion]
return &cache[acquireSequence(tr)];
˜˜˜˜˜ ^˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜
TranscriptSequence.cpp:81:8: warning: implicit conversion changes signedness: 'long' to 'size_type' (aka 'unsigned long') [-Wsign-conversion]
trs[tr].lastUse = useCounter++;
˜˜˜ ^˜
TranscriptSequence.cpp:86:26: warning: implicit conversion changes signedness: 'long' to 'size_type' (aka 'unsigned long') [-Wsign-conversion]
if(start>=(long)cache[trI].size())return string(l,'N');
˜˜˜˜˜ ^˜˜
TranscriptSequence.cpp:86:52: warning: implicit conversion changes signedness: 'long' to 'size_type' (aka 'unsigned long') [-Wsign-conversion]
if(start>=(long)cache[trI].size())return string(l,'N');
˜˜˜˜˜˜ ^
TranscriptSequence.cpp:91:18: warning: implicit conversion changes signedness: 'long' to 'size_type' (aka 'unsigned long') [-Wsign-conversion]
ret.assign(-start,'N');
˜˜˜ ^˜˜˜˜˜
TranscriptSequence.cpp:92:18: warning: implicit conversion changes signedness: 'long' to 'size_type' (aka 'unsigned long') [-Wsign-conversion]
ret+=cache[trI].substr(0,l+start);
˜˜˜˜˜ ^˜˜
TranscriptSequence.cpp:92:33: warning: implicit conversion changes signedness: 'long' to 'size_type' (aka 'unsigned long') [-Wsign-conversion]
ret+=cache[trI].substr(0,l+start);
˜˜˜˜˜ ˜^˜˜˜˜˜
TranscriptSequence.cpp:94:19: warning: implicit conversion changes signedness: 'long' to 'size_type' (aka 'unsigned long') [-Wsign-conversion]
ret = cache[trI].substr(start,l);
˜˜˜˜˜ ^˜˜
TranscriptSequence.cpp:94:31: warning: implicit conversion changes signedness: 'long' to 'size_type' (aka 'unsigned long') [-Wsign-conversion]
ret = cache[trI].substr(start,l);
˜˜˜˜˜ ^˜˜˜˜
TranscriptSequence.cpp:94:37: warning: implicit conversion changes signedness: 'long' to 'size_type' (aka 'unsigned long') [-Wsign-conversion]
ret = cache[trI].substr(start,l);
˜˜˜˜˜ ^
TranscriptSequence.cpp:95:44: warning: implicit conversion changes signedness: 'long' to 'unsigned long' [-Wsign-conversion]
if(((long)ret.size()) < l)ret.append(l-ret.size(), 'N');
^˜
TranscriptSequence.cpp:104:18: warning: implicit conversion changes signedness: 'long' to 'size_type' (aka 'unsigned long') [-Wsign-conversion]
if((ret[i]=='A')||(ret[i]=='a'))ret[i]='T';
˜˜˜ ^
TranscriptSequence.cpp:104:33: warning: implicit conversion changes signedness: 'long' to 'size_type' (aka 'unsigned long') [-Wsign-conversion]
if((ret[i]=='A')||(ret[i]=='a'))ret[i]='T';
˜˜˜ ^
TranscriptSequence.cpp:104:46: warning: implicit conversion changes signedness: 'long' to 'size_type' (aka 'unsigned long') [-Wsign-conversion]
if((ret[i]=='A')||(ret[i]=='a'))ret[i]='T';
˜˜˜ ^
TranscriptSequence.cpp:105:23: warning: implicit conversion changes signedness: 'long' to 'size_type' (aka 'unsigned long') [-Wsign-conversion]
else if((ret[i]=='T')||(ret[i]=='t'))ret[i]='A';
˜˜˜ ^
TranscriptSequence.cpp:105:38: warning: implicit conversion changes signedness: 'long' to 'size_type' (aka 'unsigned long') [-Wsign-conversion]
else if((ret[i]=='T')||(ret[i]=='t'))ret[i]='A';
˜˜˜ ^
TranscriptSequence.cpp:105:51: warning: implicit conversion changes signedness: 'long' to 'size_type' (aka 'unsigned long') [-Wsign-conversion]
else if((ret[i]=='T')||(ret[i]=='t'))ret[i]='A';
˜˜˜ ^
TranscriptSequence.cpp:106:23: warning: implicit conversion changes signedness: 'long' to 'size_type' (aka 'unsigned long') [-Wsign-conversion]
else if((ret[i]=='C')||(ret[i]=='c'))ret[i]='G';
˜˜˜ ^
TranscriptSequence.cpp:106:38: warning: implicit conversion changes signedness: 'long' to 'size_type' (aka 'unsigned long') [-Wsign-conversion]
else if((ret[i]=='C')||(ret[i]=='c'))ret[i]='G';
˜˜˜ ^
TranscriptSequence.cpp:106:51: warning: implicit conversion changes signedness: 'long' to 'size_type' (aka 'unsigned long') [-Wsign-conversion]
else if((ret[i]=='C')||(ret[i]=='c'))ret[i]='G';
˜˜˜ ^
TranscriptSequence.cpp:107:23: warning: implicit conversion changes signedness: 'long' to 'size_type' (aka 'unsigned long') [-Wsign-conversion]
else if((ret[i]=='G')||(ret[i]=='g'))ret[i]='C';
˜˜˜ ^
TranscriptSequence.cpp:107:38: warning: implicit conversion changes signedness: 'long' to 'size_type' (aka 'unsigned long') [-Wsign-conversion]
else if((ret[i]=='G')||(ret[i]=='g'))ret[i]='C';
˜˜˜ ^
TranscriptSequence.cpp:107:51: warning: implicit conversion changes signedness: 'long' to 'size_type' (aka 'unsigned long') [-Wsign-conversion]
else if((ret[i]=='G')||(ret[i]=='g'))ret[i]='C';
˜˜˜ ^
TranscriptSequence.cpp:113:11: warning: implicit conversion changes signedness: 'long' to 'size_type' (aka 'unsigned long') [-Wsign-conversion]
if(trs[tr].cache!=-1)return trs[tr].cache;
˜˜˜ ^˜
TranscriptSequence.cpp:113:36: warning: implicit conversion changes signedness: 'long' to 'size_type' (aka 'unsigned long') [-Wsign-conversion]
if(trs[tr].cache!=-1)return trs[tr].cache;
˜˜˜ ^˜
TranscriptSequence.cpp:125:17: warning: implicit conversion changes signedness: 'long' to 'size_type' (aka 'unsigned long') [-Wsign-conversion]
if(trs[cachedTrs[newP]].lastUse > trs[cachedTrs[j]].lastUse)newP=j;
˜˜˜ ^˜˜˜˜˜˜˜˜˜˜˜˜˜˜
TranscriptSequence.cpp:125:27: warning: implicit conversion changes signedness: 'long' to 'size_type' (aka 'unsigned long') [-Wsign-conversion]
if(trs[cachedTrs[newP]].lastUse > trs[cachedTrs[j]].lastUse)newP=j;
˜˜˜˜˜˜˜˜˜ ^˜˜˜
TranscriptSequence.cpp:125:48: warning: implicit conversion changes signedness: 'long' to 'size_type' (aka 'unsigned long') [-Wsign-conversion]
if(trs[cachedTrs[newP]].lastUse > trs[cachedTrs[j]].lastUse)newP=j;
˜˜˜ ^˜˜˜˜˜˜˜˜˜˜˜
TranscriptSequence.cpp:125:58: warning: implicit conversion changes signedness: 'long' to 'size_type' (aka 'unsigned long') [-Wsign-conversion]
if(trs[cachedTrs[newP]].lastUse > trs[cachedTrs[j]].lastUse)newP=j;
˜˜˜˜˜˜˜˜˜ ^
TranscriptSequence.cpp:128:11: warning: implicit conversion changes signedness: 'long' to 'size_type' (aka 'unsigned long') [-Wsign-conversion]
trs[cachedTrs[newP]].cache=-1;
˜˜˜ ^˜˜˜˜˜˜˜˜˜˜˜˜˜˜
TranscriptSequence.cpp:128:21: warning: implicit conversion changes signedness: 'long' to 'size_type' (aka 'unsigned long') [-Wsign-conversion]
trs[cachedTrs[newP]].cache=-1;
˜˜˜˜˜˜˜˜˜ ^˜˜˜
TranscriptSequence.cpp:129:13: warning: implicit conversion changes signedness: 'long' to 'size_type' (aka 'unsigned long') [-Wsign-conversion]
cache[newP].clear();
˜˜˜˜˜ ^˜˜˜
TranscriptSequence.cpp:132:21: warning: implicit conversion changes signedness: 'long' to 'size_type' (aka 'unsigned long') [-Wsign-conversion]
fastaF.seekg(trs[tr].seek);
˜˜˜ ^˜
TranscriptSequence.cpp:136:13: warning: implicit conversion changes signedness: 'long' to 'size_type' (aka 'unsigned long') [-Wsign-conversion]
cache[newP]+=seqLine;
˜˜˜˜˜ ^˜˜˜
TranscriptSequence.cpp:145:14: warning: implicit conversion changes signedness: 'long' to 'size_type' (aka 'unsigned long') [-Wsign-conversion]
cachedTrs[newP]=tr;
˜˜˜˜˜˜˜˜˜ ^˜˜˜
TranscriptSequence.cpp:146:8: warning: implicit conversion changes signedness: 'long' to 'size_type' (aka 'unsigned long') [-Wsign-conversion]
trs[tr].cache=newP;
˜˜˜ ^˜
45 warnings generated.
clang++ -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -DPACKAGE_NAME=\"Bitseq\" -DPACKAGE_TARNAME=\"bitseq\" -DPACKAGE_VERSION=\"1.4.x\" -DPACKAGE_STRING=\"Bitseq\ 1.4.x\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DBS_VERSION=\"1.4.2\" -DBIOC_BUILD=1 -D_USE_KNETFILE -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -I/usr/local/include -I"/Library/Frameworks/R.framework/Versions/3.0/Resources/library/Rsamtools/include" -I"/Library/Frameworks/R.framework/Versions/3.0/Resources/library/zlibbioc/include" -I. -fPIC -mtune=native -g -O2 -Wall -pedantic -Wconversion -c common.cpp -o common.o
In file included from common.cpp:4:
./common.h:17:17: warning: variadic macros are a C99 feature [-Wvariadic-macros]
#define message(...) Rprintf(__VA_ARGS__)
^
1 warning generated.
clang++ -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -DPACKAGE_NAME=\"Bitseq\" -DPACKAGE_TARNAME=\"bitseq\" -DPACKAGE_VERSION=\"1.4.x\" -DPACKAGE_STRING=\"Bitseq\ 1.4.x\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DBS_VERSION=\"1.4.2\" -DBIOC_BUILD=1 -D_USE_KNETFILE -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -I/usr/local/include -I"/Library/Frameworks/R.framework/Versions/3.0/Resources/library/Rsamtools/include" -I"/Library/Frameworks/R.framework/Versions/3.0/Resources/library/zlibbioc/include" -I. -fPIC -mtune=native -g -O2 -Wall -pedantic -Wconversion -c estimateDE.cpp -o estimateDE.o
In file included from estimateDE.cpp:10:
In file included from ./boost/random/mersenne_twister.hpp:29:
In file included from ./boost/random/detail/seed_impl.hpp:27:
In file included from ./boost/random/detail/const_mod.hpp:23:
./boost/random/detail/large_arithmetic.hpp:94:14: warning: implicit conversion changes signedness: 'int' to 'unsigned int' [-Wsign-conversion]
q -= error;
˜˜ ^˜˜˜˜
./boost/random/detail/large_arithmetic.hpp:95:21: warning: implicit conversion changes signedness: 'int' to 'unsigned long' [-Wsign-conversion]
rem = rem + error * m - diff;
^˜˜˜˜ ˜
In file included from estimateDE.cpp:10:
./boost/random/mersenne_twister.hpp:493:14: warning: 'long long' is a C++11 extension [-Wc++11-long-long]
UINT64_C(0xb5026f5aa96619e9),29,UINT64_C(0x5555555555555555),17,
^
/usr/include/stdint.h:248:23: note: expanded from macro 'UINT64_C'
#define UINT64_C(v) (v ## ULL)
^
<scratch space>:99:1: note: expanded from macro '0xb5026f5aa96619e9'
0xb5026f5aa96619e9ULL
^
In file included from estimateDE.cpp:10:
./boost/random/mersenne_twister.hpp:493:46: warning: 'long long' is a C++11 extension [-Wc++11-long-long]
UINT64_C(0xb5026f5aa96619e9),29,UINT64_C(0x5555555555555555),17,
^
/usr/include/stdint.h:248:23: note: expanded from macro 'UINT64_C'
#define UINT64_C(v) (v ## ULL)
^
<scratch space>:99:1: note: expanded from macro '0x5555555555555555'
0x5555555555555555ULL
^
In file included from estimateDE.cpp:10:
./boost/random/mersenne_twister.hpp:494:14: warning: 'long long' is a C++11 extension [-Wc++11-long-long]
UINT64_C(0x71d67fffeda60000),37,UINT64_C(0xfff7eee000000000),43,
^
/usr/include/stdint.h:248:23: note: expanded from macro 'UINT64_C'
#define UINT64_C(v) (v ## ULL)
^
<scratch space>:99:1: note: expanded from macro '0x71d67fffeda60000'
0x71d67fffeda60000ULL
^
In file included from estimateDE.cpp:10:
./boost/random/mersenne_twister.hpp:494:46: warning: 'long long' is a C++11 extension [-Wc++11-long-long]
UINT64_C(0x71d67fffeda60000),37,UINT64_C(0xfff7eee000000000),43,
^
/usr/include/stdint.h:248:23: note: expanded from macro 'UINT64_C'
#define UINT64_C(v) (v ## ULL)
^
<scratch space>:99:1: note: expanded from macro '0xfff7eee000000000'
0xfff7eee000000000ULL
^
In file included from estimateDE.cpp:10:
./boost/random/mersenne_twister.hpp:495:14: warning: 'long long' is a C++11 extension [-Wc++11-long-long]
UINT64_C(6364136223846793005)> mt19937_64;
^
/usr/include/stdint.h:248:23: note: expanded from macro 'UINT64_C'
#define UINT64_C(v) (v ## ULL)
^
<scratch space>:99:1: note: expanded from macro '6364136223846793005'
6364136223846793005ULL
^
In file included from estimateDE.cpp:16:
./common.h:17:17: warning: variadic macros are a C99 feature [-Wvariadic-macros]
#define message(...) Rprintf(__VA_ARGS__)
^
In file included from estimateDE.cpp:18:
./MyTimer.h:28:20: warning: implicit conversion changes signedness: 'long' to 'size_type' (aka 'unsigned long') [-Wsign-conversion]
times.resize(N);
˜˜˜˜˜ ^
./MyTimer.h:36:23: warning: implicit conversion changes signedness: 'long' to 'size_type' (aka 'unsigned long') [-Wsign-conversion]
times.resize(N);
˜˜˜˜˜ ^
./MyTimer.h:38:13: warning: implicit conversion changes signedness: 'long' to 'size_type' (aka 'unsigned long') [-Wsign-conversion]
times[timer]=time(NULL);
˜˜˜˜˜ ^˜˜˜˜
./MyTimer.h:43:28: warning: implicit conversion changes signedness: 'long' to 'size_type' (aka 'unsigned long') [-Wsign-conversion]
ret=time(NULL)-times[timer];
˜˜˜˜˜ ^˜˜˜˜
./MyTimer.h:46:13: warning: implicit conversion changes signedness: 'long' to 'size_type' (aka 'unsigned long') [-Wsign-conversion]
times[timer]=time(NULL);
˜˜˜˜˜ ^˜˜˜˜
./MyTimer.h:52:28: warning: implicit conversion changes signedness: 'long' to 'size_type' (aka 'unsigned long') [-Wsign-conversion]
ret=time(NULL)-times[timer];
˜˜˜˜˜ ^˜˜˜˜
./MyTimer.h:60:28: warning: implicit conversion changes signedness: 'long' to 'size_type' (aka 'unsigned long') [-Wsign-conversion]
ret=time(NULL)-times[timer];
˜˜˜˜˜ ^˜˜˜˜
./MyTimer.h:63:13: warning: implicit conversion changes signedness: 'long' to 'size_type' (aka 'unsigned long') [-Wsign-conversion]
times[timer]=time(NULL);
˜˜˜˜˜ ^˜˜˜˜
estimateDE.cpp:81:40: warning: implicit conversion changes signedness: 'long' to 'size_type' (aka 'unsigned long') [-Wsign-conversion]
vector<vector<vector<double> > > tr(C);
˜˜ ^
estimateDE.cpp:82:29: warning: implicit conversion changes signedness: 'long' to 'size_type' (aka 'unsigned long') [-Wsign-conversion]
vector<paramT> curParams(C);
˜˜˜˜˜˜˜˜˜ ^
estimateDE.cpp:83:36: warning: implicit conversion changes signedness: 'long' to 'size_type' (aka 'unsigned long') [-Wsign-conversion]
vector<vector<double> > samples(C,vector<double>(N));
˜˜˜˜˜˜˜ ^
estimateDE.cpp:83:53: warning: implicit conversion changes signedness: 'long' to 'size_type' (aka 'unsigned long') [-Wsign-conversion]
vector<vector<double> > samples(C,vector<double>(N));
˜˜˜˜˜˜ ^
estimateDE.cpp:84:24: warning: implicit conversion changes signedness: 'long' to 'size_type' (aka 'unsigned long') [-Wsign-conversion]
vector<double> vars(N);
˜˜˜˜ ^
estimateDE.cpp:85:24: warning: implicit conversion changes signedness: 'long' to 'size_type' (aka 'unsigned long') [-Wsign-conversion]
vector<double> mu_c(C);
˜˜˜˜ ^
estimateDE.cpp:99:24: warning: implicit conversion changes signedness: 'long' to 'size_type' (aka 'unsigned long') [-Wsign-conversion]
vector<double> difs(N);
˜˜˜˜ ^
estimateDE.cpp:112:19: warning: implicit conversion changes signedness: 'long' to 'size_type' (aka 'unsigned long') [-Wsign-conversion]
mu_c.assign(C,0);
˜˜˜˜ ^
estimateDE.cpp:117:31: warning: implicit conversion changes signedness: 'long' to 'size_type' (aka 'unsigned long') [-Wsign-conversion]
alpha = curParams[c].alpha + RC / 2.0;
˜˜˜˜˜˜˜˜˜ ^
estimateDE.cpp:123:26: warning: implicit conversion changes signedness: 'long' to 'size_type' (aka 'unsigned long') [-Wsign-conversion]
sum += tr[c][r][n];
˜˜ ^
estimateDE.cpp:123:29: warning: implicit conversion changes signedness: 'long' to 'size_type' (aka 'unsigned long') [-Wsign-conversion]
sum += tr[c][r][n];
˜˜ ^
estimateDE.cpp:123:32: warning: implicit conversion changes signedness: 'long' to 'size_type' (aka 'unsigned long') [-Wsign-conversion]
sum += tr[c][r][n];
˜˜ ^
estimateDE.cpp:124:28: warning: implicit conversion changes signedness: 'long' to 'size_type' (aka 'unsigned long') [-Wsign-conversion]
sumSq += tr[c][r][n]*tr[c][r][n];
˜˜ ^
estimateDE.cpp:124:31: warning: implicit conversion changes signedness: 'long' to 'size_type' (aka 'unsigned long') [-Wsign-conversion]
sumSq += tr[c][r][n]*tr[c][r][n];
˜˜ ^
estimateDE.cpp:124:34: warning: implicit conversion changes signedness: 'long' to 'size_type' (aka 'unsigned long') [-Wsign-conversion]
sumSq += tr[c][r][n]*tr[c][r][n];
˜˜ ^
estimateDE.cpp:124:40: warning: implicit conversion changes signedness: 'long' to 'size_type' (aka 'unsigned long') [-Wsign-conversion]
sumSq += tr[c][r][n]*tr[c][r][n];
˜˜ ^
estimateDE.cpp:124:43: warning: implicit conversion changes signedness: 'long' to 'size_type' (aka 'unsigned long') [-Wsign-conversion]
sumSq += tr[c][r][n]*tr[c][r][n];
˜˜ ^
estimateDE.cpp:124:46: warning: implicit conversion changes signedness: 'long' to 'size_type' (aka 'unsigned long') [-Wsign-conversion]
sumSq += tr[c][r][n]*tr[c][r][n];
˜˜ ^
estimateDE.cpp:129:30: warning: implicit conversion changes signedness: 'long' to 'size_type' (aka 'unsigned long') [-Wsign-conversion]
beta = curParams[c].beta + betaPar / 2 ;
˜˜˜˜˜˜˜˜˜ ^
estimateDE.cpp:133:20: warning: implicit conversion loses floating-point precision: 'result_type' (aka 'long double') to 'double' [-Wconversion]
prec = gammaDistribution(rng_mt);
˜ ^˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜
estimateDE.cpp:136:18: warning: implicit conversion changes signedness: 'long' to 'size_type' (aka 'unsigned long') [-Wsign-conversion]
vars[n] = var;
˜˜˜˜ ^
estimateDE.cpp:141:21: warning: implicit conversion changes signedness: 'long' to 'size_type' (aka 'unsigned long') [-Wsign-conversion]
samples[c][n] = normalDistribution(rng_mt);
˜˜˜˜˜˜˜ ^
estimateDE.cpp:141:24: warning: implicit conversion changes signedness: 'long' to 'size_type' (aka 'unsigned long') [-Wsign-conversion]
samples[c][n] = normalDistribution(rng_mt);
˜˜˜˜˜˜˜ ^
estimateDE.cpp:141:29: warning: implicit conversion loses floating-point precision: 'result_type' (aka 'long double') to 'double' [-Wconversion]
samples[c][n] = normalDistribution(rng_mt);
˜ ^˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜
estimateDE.cpp:142:18: warning: implicit conversion changes signedness: 'long' to 'size_type' (aka 'unsigned long') [-Wsign-conversion]
mu_c[c] += samples[c][n];
˜˜˜˜ ^
estimateDE.cpp:142:32: warning: implicit conversion changes signedness: 'long' to 'size_type' (aka 'unsigned long') [-Wsign-conversion]
mu_c[c] += samples[c][n];
˜˜˜˜˜˜˜ ^
estimateDE.cpp:142:35: warning: implicit conversion changes signedness: 'long' to 'size_type' (aka 'unsigned long') [-Wsign-conversion]
mu_c[c] += samples[c][n];
˜˜˜˜˜˜˜ ^
estimateDE.cpp:148:29: warning: implicit conversion changes signedness: 'long' to 'size_type' (aka 'unsigned long') [-Wsign-conversion]
for(c=0;c<C;c++) mu_c[c] /= N;
˜˜˜˜ ^
estimateDE.cpp:154:27: warning: implicit conversion changes signedness: 'long' to 'size_type' (aka 'unsigned long') [-Wsign-conversion]
if(samples[c2][n] > samples[c][n])pplr+=1;
˜˜˜˜˜˜˜ ^˜
estimateDE.cpp:154:31: warning: implicit conversion changes signedness: 'long' to 'size_type' (aka 'unsigned long') [-Wsign-conversion]
if(samples[c2][n] > samples[c][n])pplr+=1;
˜˜˜˜˜˜˜ ^
estimateDE.cpp:154:44: warning: implicit conversion changes signedness: 'long' to 'size_type' (aka 'unsigned long') [-Wsign-conversion]
if(samples[c2][n] > samples[c][n])pplr+=1;
˜˜˜˜˜˜˜ ^
estimateDE.cpp:154:47: warning: implicit conversion changes signedness: 'long' to 'size_type' (aka 'unsigned long') [-Wsign-conversion]
if(samples[c2][n] > samples[c][n])pplr+=1;
˜˜˜˜˜˜˜ ^
estimateDE.cpp:164:21: warning: implicit conversion changes signedness: 'long' to 'size_type' (aka 'unsigned long') [-Wsign-conversion]
difs[n] = samples[c2][n]-samples[c][n];
˜˜˜˜ ^
estimateDE.cpp:164:34: warning: implicit conversion changes signedness: 'long' to 'size_type' (aka 'unsigned long') [-Wsign-conversion]
difs[n] = samples[c2][n]-samples[c][n];
˜˜˜˜˜˜˜ ^˜
estimateDE.cpp:164:38: warning: implicit conversion changes signedness: 'long' to 'size_type' (aka 'unsigned long') [-Wsign-conversion]
difs[n] = samples[c2][n]-samples[c][n];
˜˜˜˜˜˜˜ ^
estimateDE.cpp:164:49: warning: implicit conversion changes signedness: 'long' to 'size_type' (aka 'unsigned long') [-Wsign-conversion]
difs[n] = samples[c2][n]-samples[c][n];
˜˜˜˜˜˜˜ ^
estimateDE.cpp:164:52: warning: implicit conversion changes signedness: 'long' to 'size_type' (aka 'unsigned long') [-Wsign-conversion]
difs[n] = samples[c2][n]-samples[c][n];
˜˜˜˜˜˜˜ ^
estimateDE.cpp:168:28: warning: implicit conversion changes signedness: 'long' to 'size_type' (aka 'unsigned long') [-Wsign-conversion]
log2FC = (mu_c[c2] - mu_c[c])/log(2);
˜˜˜˜ ^˜
estimateDE.cpp:168:39: warning: implicit conversion changes signedness: 'long' to 'size_type' (aka 'unsigned long') [-Wsign-conversion]
log2FC = (mu_c[c2] - mu_c[c])/log(2);
˜˜˜˜ ^
estimateDE.cpp:174:42: warning: implicit conversion changes signedness: 'long' to 'size_type' (aka 'unsigned long') [-Wsign-conversion]
for(c = 0; c < C-1; c++)outF<<mu_c[c]<<" ";
˜˜˜˜ ^
estimateDE.cpp:175:19: warning: implicit conversion changes signedness: 'long' to 'size_type' (aka 'unsigned long') [-Wsign-conversion]
outF<<mu_c[C-1]<<endl;
˜˜˜˜ ˜^˜
estimateDE.cpp:180:50: warning: implicit conversion changes signedness: 'long' to 'size_type' (aka 'unsigned long') [-Wsign-conversion]
for(n=0;n<N;n++)outFiles[c]<<samples[c][n]<<" ";
˜˜˜˜˜˜˜ ^
estimateDE.cpp:180:53: warning: implicit conversion changes signedness: 'long' to 'size_type' (aka 'unsigned long') [-Wsign-conversion]
for(n=0;n<N;n++)outFiles[c]<<samples[c][n]<<" ";
˜˜˜˜˜˜˜ ^
estimateDE.cpp:184:45: warning: implicit conversion changes signedness: 'long' to 'size_type' (aka 'unsigned long') [-Wsign-conversion]
for(n=0;n<N;n++) outFiles[C]<<vars[n]<<" ";
˜˜˜˜ ^
estimateDE.cpp:93:35: warning: implicit conversion loses integer precision: 'long' to 'const unsigned int' [-Wshorten-64-to-32]
boost::random::mt11213b rng_mt(ns_misc::getSeed(args));
˜˜˜˜˜˜ ^˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜
estimateDE.cpp:227:38: warning: implicit conversion changes signedness: 'long' to 'size_type' (aka 'unsigned long') [-Wsign-conversion]
outFiles[c]<<args.args()[i]<<" ";
˜˜˜˜ ^
estimateDE.cpp:254:26: warning: implicit conversion changes signedness: 'long' to 'size_type' (aka 'unsigned long') [-Wsign-conversion]
*outF<<args.args()[i]<<" ";
˜˜˜˜ ^
estimateDE.cpp:271:28: warning: implicit conversion changes signedness: 'unsigned long' to 'long' [-Wsign-conversion]
long i=0,j=params.size()-1,k;
˜ ˜˜˜˜˜˜˜˜˜˜˜˜˜^˜
estimateDE.cpp:277:20: warning: implicit conversion changes signedness: 'long' to 'size_type' (aka 'unsigned long') [-Wsign-conversion]
if(expr>=params[j].expr){
˜˜˜˜˜˜ ^
estimateDE.cpp:278:25: warning: implicit conversion changes signedness: 'long' to 'size_type' (aka 'unsigned long') [-Wsign-conversion]
par->alpha=params[j].alpha;
˜˜˜˜˜˜ ^
estimateDE.cpp:279:24: warning: implicit conversion changes signedness: 'long' to 'size_type' (aka 'unsigned long') [-Wsign-conversion]
par->beta=params[j].beta;
˜˜˜˜˜˜ ^
estimateDE.cpp:284:17: warning: implicit conversion changes signedness: 'long' to 'size_type' (aka 'unsigned long') [-Wsign-conversion]
if(params[k].expr<=expr)i=k;
˜˜˜˜˜˜ ^
estimateDE.cpp:287:19: warning: implicit conversion changes signedness: 'long' to 'size_type' (aka 'unsigned long') [-Wsign-conversion]
if(expr-params[i].expr<params[j].expr-expr)k=i;
˜˜˜˜˜˜ ^
estimateDE.cpp:287:34: warning: implicit conversion changes signedness: 'long' to 'size_type' (aka 'unsigned long') [-Wsign-conversion]
if(expr-params[i].expr<params[j].expr-expr)k=i;
˜˜˜˜˜˜ ^
estimateDE.cpp:290:22: warning: implicit conversion changes signedness: 'long' to 'size_type' (aka 'unsigned long') [-Wsign-conversion]
par->alpha=params[k].alpha;
˜˜˜˜˜˜ ^
estimateDE.cpp:291:21: warning: implicit conversion changes signedness: 'long' to 'size_type' (aka 'unsigned long') [-Wsign-conversion]
par->beta=params[k].beta;
˜˜˜˜˜˜ ^
estimateDE.cpp:302:22: warning: implicit conversion changes signedness: 'long' to 'size_type' (aka 'unsigned long') [-Wsign-conversion]
if((long)(*tr)[c].size() < RC){
˜ ^
estimateDE.cpp:303:16: warning: implicit conversion changes signedness: 'long' to 'size_type' (aka 'unsigned long') [-Wsign-conversion]
(*tr)[c].resize( RC );
˜ ^
estimateDE.cpp:303:27: warning: implicit conversion changes signedness: 'long' to 'size_type' (aka 'unsigned long') [-Wsign-conversion]
(*tr)[c].resize( RC );
˜ ^˜
estimateDE.cpp:306:49: warning: implicit conversion changes signedness: 'long' to 'size_type' (aka 'unsigned long') [-Wsign-conversion]
if(cond->getTranscript(c, r , m, (*tr)[c][r]), N){
˜ ^
estimateDE.cpp:306:52: warning: implicit conversion changes signedness: 'long' to 'size_type' (aka 'unsigned long') [-Wsign-conversion]
if(cond->getTranscript(c, r , m, (*tr)[c][r]), N){
˜ ^
estimateDE.cpp:309:41: warning: implicit conversion changes signedness: 'long' to 'size_type' (aka 'unsigned long') [-Wsign-conversion]
if(!cond->logged())(*tr)[c][r][n] = ((*tr)[c][r][n] == 0)? ns_misc::LOG_ZERO : log ((*tr)[c][r][n] );
˜ ^
estimateDE.cpp:309:44: warning: implicit conversion changes signedness: 'long' to 'size_type' (aka 'unsigned long') [-Wsign-conversion]
if(!cond->logged())(*tr)[c][r][n] = ((*tr)[c][r][n] == 0)? ns_misc::LOG_ZERO : log ((*tr)[c][r][n] );
˜ ^
estimateDE.cpp:309:47: warning: implicit conversion changes signedness: 'long' to 'size_type' (aka 'unsigned long') [-Wsign-conversion]
if(!cond->logged())(*tr)[c][r][n] = ((*tr)[c][r][n] == 0)? ns_misc::LOG_ZERO : log ((*tr)[c][r][n] );
˜ ^
estimateDE.cpp:309:59: warning: implicit conversion changes signedness: 'long' to 'size_type' (aka 'unsigned long') [-Wsign-conversion]
if(!cond->logged())(*tr)[c][r][n] = ((*tr)[c][r][n] == 0)? ns_misc::LOG_ZERO : log ((*tr)[c][r][n] );
˜ ^
estimateDE.cpp:309:62: warning: implicit conversion changes signedness: 'long' to 'size_type' (aka 'unsigned long') [-Wsign-conversion]
if(!cond->logged())(*tr)[c][r][n] = ((*tr)[c][r][n] == 0)? ns_misc::LOG_ZERO : log ((*tr)[c][r][n] );
˜ ^
estimateDE.cpp:309:65: warning: implicit conversion changes signedness: 'long' to 'size_type' (aka 'unsigned long') [-Wsign-conversion]
if(!cond->logged())(*tr)[c][r][n] = ((*tr)[c][r][n] == 0)? ns_misc::LOG_ZERO : log ((*tr)[c][r][n] );
˜ ^
estimateDE.cpp:309:106: warning: implicit conversion changes signedness: 'long' to 'size_type' (aka 'unsigned long') [-Wsign-conversion]
if(!cond->logged())(*tr)[c][r][n] = ((*tr)[c][r][n] == 0)? ns_misc::LOG_ZERO : log ((*tr)[c][r][n] );
˜ ^
estimateDE.cpp:309:109: warning: implicit conversion changes signedness: 'long' to 'size_type' (aka 'unsigned long') [-Wsign-conversion]
if(!cond->logged())(*tr)[c][r][n] = ((*tr)[c][r][n] == 0)? ns_misc::LOG_ZERO : log ((*tr)[c][r][n] );
˜ ^
estimateDE.cpp:309:112: warning: implicit conversion changes signedness: 'long' to 'size_type' (aka 'unsigned long') [-Wsign-conversion]
if(!cond->logged())(*tr)[c][r][n] = ((*tr)[c][r][n] == 0)? ns_misc::LOG_ZERO : log ((*tr)[c][r][n] );
˜ ^
estimateDE.cpp:310:28: warning: implicit conversion changes signedness: 'long' to 'size_type' (aka 'unsigned long') [-Wsign-conversion]
mu_0+=(*tr)[c][r][n];
˜ ^
estimateDE.cpp:310:31: warning: implicit conversion changes signedness: 'long' to 'size_type' (aka 'unsigned long') [-Wsign-conversion]
mu_0+=(*tr)[c][r][n];
˜ ^
estimateDE.cpp:310:34: warning: implicit conversion changes signedness: 'long' to 'size_type' (aka 'unsigned long') [-Wsign-conversion]
mu_0+=(*tr)[c][r][n];
˜ ^
estimateDE.cpp:323:45: warning: implicit conversion changes signedness: 'long' to 'size_type' (aka 'unsigned long') [-Wsign-conversion]
getParams(mu_0, params, &(*curParams)[c]);
˜ ^
90 warnings generated.
clang++ -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -DPACKAGE_NAME=\"Bitseq\" -DPACKAGE_TARNAME=\"bitseq\" -DPACKAGE_VERSION=\"1.4.x\" -DPACKAGE_STRING=\"Bitseq\ 1.4.x\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DBS_VERSION=\"1.4.2\" -DBIOC_BUILD=1 -D_USE_KNETFILE -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -I/usr/local/include -I"/Library/Frameworks/R.framework/Versions/3.0/Resources/library/Rsamtools/include" -I"/Library/Frameworks/R.framework/Versions/3.0/Resources/library/zlibbioc/include" -I. -fPIC -mtune=native -g -O2 -Wall -pedantic -Wconversion -c estimateExpression.cpp -o estimateExpression.o
In file included from estimateExpression.cpp:8:
In file included from ./CollapsedSampler.h:3:
In file included from ./Sampler.h:6:
In file included from ./boost/random/mersenne_twister.hpp:29:
In file included from ./boost/random/detail/seed_impl.hpp:27:
In file included from ./boost/random/detail/const_mod.hpp:23:
./boost/random/detail/large_arithmetic.hpp:94:14: warning: implicit conversion changes signedness: 'int' to 'unsigned int' [-Wsign-conversion]
q -= error;
˜˜ ^˜˜˜˜
./boost/random/detail/large_arithmetic.hpp:95:21: warning: implicit conversion changes signedness: 'int' to 'unsigned long' [-Wsign-conversion]
rem = rem + error * m - diff;
^˜˜˜˜ ˜
In file included from estimateExpression.cpp:8:
In file included from ./CollapsedSampler.h:3:
In file included from ./Sampler.h:6:
./boost/random/mersenne_twister.hpp:493:14: warning: 'long long' is a C++11 extension [-Wc++11-long-long]
UINT64_C(0xb5026f5aa96619e9),29,UINT64_C(0x5555555555555555),17,
^
/usr/include/stdint.h:248:23: note: expanded from macro 'UINT64_C'
#define UINT64_C(v) (v ## ULL)
^
<scratch space>:92:1: note: expanded from macro '0xb5026f5aa96619e9'
0xb5026f5aa96619e9ULL
^
In file included from estimateExpression.cpp:8:
In file included from ./CollapsedSampler.h:3:
In file included from ./Sampler.h:6:
./boost/random/mersenne_twister.hpp:493:46: warning: 'long long' is a C++11 extension [-Wc++11-long-long]
UINT64_C(0xb5026f5aa96619e9),29,UINT64_C(0x5555555555555555),17,
^
/usr/include/stdint.h:248:23: note: expanded from macro 'UINT64_C'
#define UINT64_C(v) (v ## ULL)
^
<scratch space>:92:1: note: expanded from macro '0x5555555555555555'
0x5555555555555555ULL
^
In file included from estimateExpression.cpp:8:
In file included from ./CollapsedSampler.h:3:
In file included from ./Sampler.h:6:
./boost/random/mersenne_twister.hpp:494:14: warning: 'long long' is a C++11 extension [-Wc++11-long-long]
UINT64_C(0x71d67fffeda60000),37,UINT64_C(0xfff7eee000000000),43,
^
/usr/include/stdint.h:248:23: note: expanded from macro 'UINT64_C'
#define UINT64_C(v) (v ## ULL)
^
<scratch space>:92:1: note: expanded from macro '0x71d67fffeda60000'
0x71d67fffeda60000ULL
^
In file included from estimateExpression.cpp:8:
In file included from ./CollapsedSampler.h:3:
In file included from ./Sampler.h:6:
./boost/random/mersenne_twister.hpp:494:46: warning: 'long long' is a C++11 extension [-Wc++11-long-long]
UINT64_C(0x71d67fffeda60000),37,UINT64_C(0xfff7eee000000000),43,
^
/usr/include/stdint.h:248:23: note: expanded from macro 'UINT64_C'
#define UINT64_C(v) (v ## ULL)
^
<scratch space>:92:1: note: expanded from macro '0xfff7eee000000000'
0xfff7eee000000000ULL
^
In file included from estimateExpression.cpp:8:
In file included from ./CollapsedSampler.h:3:
In file included from ./Sampler.h:6:
./boost/random/mersenne_twister.hpp:495:14: warning: 'long long' is a C++11 extension [-Wc++11-long-long]
UINT64_C(6364136223846793005)> mt19937_64;
^
/usr/include/stdint.h:248:23: note: expanded from macro 'UINT64_C'
#define UINT64_C(v) (v ## ULL)
^
<scratch space>:92:1: note: expanded from macro '6364136223846793005'
6364136223846793005ULL
^
In file included from estimateExpression.cpp:12:
In file included from ./MyTimer.h:10:
./common.h:17:17: warning: variadic macros are a C99 feature [-Wvariadic-macros]
#define message(...) Rprintf(__VA_ARGS__)
^
In file included from estimateExpression.cpp:12:
./MyTimer.h:28:20: warning: implicit conversion changes signedness: 'long' to 'size_type' (aka 'unsigned long') [-Wsign-conversion]
times.resize(N);
˜˜˜˜˜ ^
./MyTimer.h:36:23: warning: implicit conversion changes signedness: 'long' to 'size_type' (aka 'unsigned long') [-Wsign-conversion]
times.resize(N);
˜˜˜˜˜ ^
./MyTimer.h:38:13: warning: implicit conversion changes signedness: 'long' to 'size_type' (aka 'unsigned long') [-Wsign-conversion]
times[timer]=time(NULL);
˜˜˜˜˜ ^˜˜˜˜
./MyTimer.h:43:28: warning: implicit conversion changes signedness: 'long' to 'size_type' (aka 'unsigned long') [-Wsign-conversion]
ret=time(NULL)-times[timer];
˜˜˜˜˜ ^˜˜˜˜
./MyTimer.h:46:13: warning: implicit conversion changes signedness: 'long' to 'size_type' (aka 'unsigned long') [-Wsign-conversion]
times[timer]=time(NULL);
˜˜˜˜˜ ^˜˜˜˜
./MyTimer.h:52:28: warning: implicit conversion changes signedness: 'long' to 'size_type' (aka 'unsigned long') [-Wsign-conversion]
ret=time(NULL)-times[timer];
˜˜˜˜˜ ^˜˜˜˜
./MyTimer.h:60:28: warning: implicit conversion changes signedness: 'long' to 'size_type' (aka 'unsigned long') [-Wsign-conversion]
ret=time(NULL)-times[timer];
˜˜˜˜˜ ^˜˜˜˜
./MyTimer.h:63:13: warning: implicit conversion changes signedness: 'long' to 'size_type' (aka 'unsigned long') [-Wsign-conversion]
times[timer]=time(NULL);
˜˜˜˜˜ ^˜˜˜˜
estimateExpression.cpp:152:26: warning: implicit conversion changes signedness: 'long' to 'size_type' (aka 'unsigned long') [-Wsign-conversion]
vector<pairD> betwVar(M),withVar(M),s2j(M),totAverage(M),av,var;
˜˜˜˜˜˜˜ ^
estimateExpression.cpp:152:37: warning: implicit conversion changes signedness: 'long' to 'size_type' (aka 'unsigned long') [-Wsign-conversion]
vector<pairD> betwVar(M),withVar(M),s2j(M),totAverage(M),av,var;
˜˜˜˜˜˜˜ ^
estimateExpression.cpp:152:44: warning: implicit conversion changes signedness: 'long' to 'size_type' (aka 'unsigned long') [-Wsign-conversion]
vector<pairD> betwVar(M),withVar(M),s2j(M),totAverage(M),av,var;
˜˜˜ ^
estimateExpression.cpp:152:58: warning: implicit conversion changes signedness: 'long' to 'size_type' (aka 'unsigned long') [-Wsign-conversion]
vector<pairD> betwVar(M),withVar(M),s2j(M),totAverage(M),av,var;
˜˜˜˜˜˜˜˜˜˜ ^
estimateExpression.cpp:153:36: warning: implicit conversion changes signedness: 'long' to 'size_type' (aka 'unsigned long') [-Wsign-conversion]
vector<pair<pairD,long> > rHat2(M);
˜˜˜˜˜ ^
estimateExpression.cpp:161:30: warning: implicit conversion changes signedness: 'long' to 'size_type' (aka 'unsigned long') [-Wsign-conversion]
vector<Sampler*> samplers(chainsN);
˜˜˜˜˜˜˜˜ ^˜˜˜˜˜˜
estimateExpression.cpp:164:19: warning: implicit conversion changes signedness: 'long' to 'size_type' (aka 'unsigned long') [-Wsign-conversion]
samplers[j] = new CollapsedSampler;
˜˜˜˜˜˜˜˜ ^
estimateExpression.cpp:167:19: warning: implicit conversion changes signedness: 'long' to 'size_type' (aka 'unsigned long') [-Wsign-conversion]
samplers[j] = new GibbsSampler;
˜˜˜˜˜˜˜˜ ^
estimateExpression.cpp:177:16: warning: implicit conversion changes signedness: 'long' to 'size_type' (aka 'unsigned long') [-Wsign-conversion]
samplers[i]->noSave();
˜˜˜˜˜˜˜˜ ^
estimateExpression.cpp:179:16: warning: implicit conversion changes signedness: 'long' to 'size_type' (aka 'unsigned long') [-Wsign-conversion]
samplers[i]->init(M, samplesN, samplesSave, Nunmap, alignments, gPar.beta(), gPar.dir(), seed);
˜˜˜˜˜˜˜˜ ^
estimateExpression.cpp:190:15: warning: unknown pragma ignored [-Wunknown-pragmas]
#pragma omp parallel for private(subCounter)
^
estimateExpression.cpp:193:21: warning: implicit conversion changes signedness: 'long' to 'size_type' (aka 'unsigned long') [-Wsign-conversion]
samplers[i]->sample();
˜˜˜˜˜˜˜˜ ^
estimateExpression.cpp:211:16: warning: implicit conversion changes signedness: 'long' to 'size_type' (aka 'unsigned long') [-Wsign-conversion]
samplers[i]->resetSampler(samplesN);
˜˜˜˜˜˜˜˜ ^
estimateExpression.cpp:225:18: warning: unknown pragma ignored [-Wunknown-pragmas]
#pragma omp parallel for private(subCounter)
^
estimateExpression.cpp:228:25: warning: implicit conversion changes signedness: 'long' to 'size_type' (aka 'unsigned long') [-Wsign-conversion]
samplers[i]->sample();
˜˜˜˜˜˜˜˜ ^
estimateExpression.cpp:229:25: warning: implicit conversion changes signedness: 'long' to 'size_type' (aka 'unsigned long') [-Wsign-conversion]
samplers[i]->update();
˜˜˜˜˜˜˜˜ ^
estimateExpression.cpp:252:25: warning: implicit conversion changes signedness: 'long' to 'size_type' (aka 'unsigned long') [-Wsign-conversion]
totAverage.assign(M,pairD(0,0));
˜˜˜˜˜˜˜˜˜˜ ^
estimateExpression.cpp:253:22: warning: implicit conversion changes signedness: 'long' to 'size_type' (aka 'unsigned long') [-Wsign-conversion]
betwVar.assign(M,pairD(0,0));
˜˜˜˜˜˜˜ ^
estimateExpression.cpp:254:22: warning: implicit conversion changes signedness: 'long' to 'size_type' (aka 'unsigned long') [-Wsign-conversion]
withVar.assign(M,pairD(0,0));
˜˜˜˜˜˜˜ ^
estimateExpression.cpp:258:29: warning: implicit conversion changes signedness: 'long' to 'size_type' (aka 'unsigned long') [-Wsign-conversion]
tmpA = samplers[j]->getAverage(i);
˜˜˜˜˜˜˜˜ ^
estimateExpression.cpp:259:29: warning: implicit conversion changes signedness: 'long' to 'size_type' (aka 'unsigned long') [-Wsign-conversion]
tmpV = samplers[j]->getWithinVariance(i);
˜˜˜˜˜˜˜˜ ^
estimateExpression.cpp:260:24: warning: implicit conversion changes signedness: 'long' to 'size_type' (aka 'unsigned long') [-Wsign-conversion]
totAverage[i].FF += tmpA.FF;
˜˜˜˜˜˜˜˜˜˜ ^
estimateExpression.cpp:261:24: warning: implicit conversion changes signedness: 'long' to 'size_type' (aka 'unsigned long') [-Wsign-conversion]
totAverage[i].SS += tmpA.SS;
˜˜˜˜˜˜˜˜˜˜ ^
estimateExpression.cpp:262:21: warning: implicit conversion changes signedness: 'long' to 'size_type' (aka 'unsigned long') [-Wsign-conversion]
withVar[i].FF += tmpV.FF;
˜˜˜˜˜˜˜ ^
estimateExpression.cpp:263:21: warning: implicit conversion changes signedness: 'long' to 'size_type' (aka 'unsigned long') [-Wsign-conversion]
withVar[i].SS += tmpV.SS;
˜˜˜˜˜˜˜ ^
estimateExpression.cpp:265:21: warning: implicit conversion changes signedness: 'long' to 'size_type' (aka 'unsigned long') [-Wsign-conversion]
totAverage[i].FF /= chainsN;
˜˜˜˜˜˜˜˜˜˜ ^
estimateExpression.cpp:266:21: warning: implicit conversion changes signedness: 'long' to 'size_type' (aka 'unsigned long') [-Wsign-conversion]
totAverage[i].SS /= chainsN;
˜˜˜˜˜˜˜˜˜˜ ^
estimateExpression.cpp:267:18: warning: implicit conversion changes signedness: 'long' to 'size_type' (aka 'unsigned long') [-Wsign-conversion]
withVar[i].FF /= chainsN;
˜˜˜˜˜˜˜ ^
estimateExpression.cpp:268:18: warning: implicit conversion changes signedness: 'long' to 'size_type' (aka 'unsigned long') [-Wsign-conversion]
withVar[i].SS /= chainsN;
˜˜˜˜˜˜˜ ^
estimateExpression.cpp:270:29: warning: implicit conversion changes signedness: 'long' to 'size_type' (aka 'unsigned long') [-Wsign-conversion]
tmpA = samplers[j]->getAverage(i);
˜˜˜˜˜˜˜˜ ^
estimateExpression.cpp:271:21: warning: implicit conversion changes signedness: 'long' to 'size_type' (aka 'unsigned long') [-Wsign-conversion]
betwVar[i].FF += (totAverage[i].FF - tmpA.FF)*(totAverage[i].FF - tmpA.FF);
˜˜˜˜˜˜˜ ^
estimateExpression.cpp:271:42: warning: implicit conversion changes signedness: 'long' to 'size_type' (aka 'unsigned long') [-Wsign-conversion]
betwVar[i].FF += (totAverage[i].FF - tmpA.FF)*(totAverage[i].FF - tmpA.FF);
˜˜˜˜˜˜˜˜˜˜ ^
estimateExpression.cpp:271:71: warning: implicit conversion changes signedness: 'long' to 'size_type' (aka 'unsigned long') [-Wsign-conversion]
betwVar[i].FF += (totAverage[i].FF - tmpA.FF)*(totAverage[i].FF - tmpA.FF);
˜˜˜˜˜˜˜˜˜˜ ^
estimateExpression.cpp:272:21: warning: implicit conversion changes signedness: 'long' to 'size_type' (aka 'unsigned long') [-Wsign-conversion]
betwVar[i].SS += (totAverage[i].SS - tmpA.SS)*(totAverage[i].SS - tmpA.SS);
˜˜˜˜˜˜˜ ^
estimateExpression.cpp:272:42: warning: implicit conversion changes signedness: 'long' to 'size_type' (aka 'unsigned long') [-Wsign-conversion]
betwVar[i].SS += (totAverage[i].SS - tmpA.SS)*(totAverage[i].SS - tmpA.SS);
˜˜˜˜˜˜˜˜˜˜ ^
estimateExpression.cpp:272:71: warning: implicit conversion changes signedness: 'long' to 'size_type' (aka 'unsigned long') [-Wsign-conversion]
betwVar[i].SS += (totAverage[i].SS - tmpA.SS)*(totAverage[i].SS - tmpA.SS);
˜˜˜˜˜˜˜˜˜˜ ^
estimateExpression.cpp:274:18: warning: implicit conversion changes signedness: 'long' to 'size_type' (aka 'unsigned long') [-Wsign-conversion]
betwVar[i].FF /= (chainsN-1.0);
˜˜˜˜˜˜˜ ^
estimateExpression.cpp:275:18: warning: implicit conversion changes signedness: 'long' to 'size_type' (aka 'unsigned long') [-Wsign-conversion]
betwVar[i].SS /= (chainsN-1.0);
˜˜˜˜˜˜˜ ^
estimateExpression.cpp:279:16: warning: implicit conversion changes signedness: 'long' to 'size_type' (aka 'unsigned long') [-Wsign-conversion]
rHat2[i].SS=i;
˜˜˜˜˜ ^
estimateExpression.cpp:280:21: warning: implicit conversion changes signedness: 'long' to 'size_type' (aka 'unsigned long') [-Wsign-conversion]
if(withVar[i].FF == 0 ){
˜˜˜˜˜˜˜ ^
estimateExpression.cpp:281:19: warning: implicit conversion changes signedness: 'long' to 'size_type' (aka 'unsigned long') [-Wsign-conversion]
rHat2[i].FF.FF = 0;
˜˜˜˜˜ ^
estimateExpression.cpp:282:19: warning: implicit conversion changes signedness: 'long' to 'size_type' (aka 'unsigned long') [-Wsign-conversion]
rHat2[i].FF.SS = 0;
˜˜˜˜˜ ^
estimateExpression.cpp:284:19: warning: implicit conversion changes signedness: 'long' to 'size_type' (aka 'unsigned long') [-Wsign-conversion]
rHat2[i].FF.FF = (samplesHave - 1.0) / samplesHave + betwVar[i].FF / withVar[i].FF ;
˜˜˜˜˜ ^
estimateExpression.cpp:284:74: warning: implicit conversion changes signedness: 'long' to 'size_type' (aka 'unsigned long') [-Wsign-conversion]
rHat2[i].FF.FF = (samplesHave - 1.0) / samplesHave + betwVar[i].FF / withVar[i].FF ;
˜˜˜˜˜˜˜ ^
estimateExpression.cpp:284:90: warning: implicit conversion changes signedness: 'long' to 'size_type' (aka 'unsigned long') [-Wsign-conversion]
rHat2[i].FF.FF = (samplesHave - 1.0) / samplesHave + betwVar[i].FF / withVar[i].FF ;
˜˜˜˜˜˜˜ ^
estimateExpression.cpp:285:19: warning: implicit conversion changes signedness: 'long' to 'size_type' (aka 'unsigned long') [-Wsign-conversion]
rHat2[i].FF.SS = (samplesHave - 1.0) / samplesHave + betwVar[i].SS / withVar[i].SS ;
˜˜˜˜˜ ^
estimateExpression.cpp:285:74: warning: implicit conversion changes signedness: 'long' to 'size_type' (aka 'unsigned long') [-Wsign-conversion]
rHat2[i].FF.SS = (samplesHave - 1.0) / samplesHave + betwVar[i].SS / withVar[i].SS ;
˜˜˜˜˜˜˜ ^
estimateExpression.cpp:285:90: warning: implicit conversion changes signedness: 'long' to 'size_type' (aka 'unsigned long') [-Wsign-conversion]
rHat2[i].FF.SS = (samplesHave - 1.0) / samplesHave + betwVar[i].SS / withVar[i].SS ;
˜˜˜˜˜˜˜ ^
estimateExpression.cpp:295:27: warning: implicit conversion changes signedness: 'long' to 'size_type' (aka 'unsigned long') [-Wsign-conversion]
rH1 = sqrt(rHat2[i].FF.FF);
˜˜˜˜˜ ^
estimateExpression.cpp:296:27: warning: implicit conversion changes signedness: 'long' to 'size_type' (aka 'unsigned long') [-Wsign-conversion]
rH2 = sqrt(rHat2[i].FF.SS);
˜˜˜˜˜ ^
estimateExpression.cpp:301:72: warning: implicit conversion changes signedness: 'long' to 'size_type' (aka 'unsigned long') [-Wsign-conversion]
message(" %7.4lf (%7.4lf | %6ld | %7.4lf)",rH1,rH2,rHat2[i].SS-1,totAverage[rHat2[i].SS].FF);
˜˜˜˜˜ ^
./common.h:17:30: note: expanded from macro 'message'
#define message(...) Rprintf(__VA_ARGS__)
^
estimateExpression.cpp:301:100: warning: implicit conversion changes signedness: 'long' to 'size_type' (aka 'unsigned long') [-Wsign-conversion]
message(" %7.4lf (%7.4lf | %6ld | %7.4lf)",rH1,rH2,rHat2[i].SS-1,totAverage[rHat2[i].SS].FF);
˜˜˜˜˜˜˜˜˜˜ ˜˜˜˜˜˜˜˜˜^˜
estimateExpression.cpp:22:12: note: expanded from macro 'SS'
#define SS second
^
./common.h:17:30: note: expanded from macro 'message'
#define message(...) Rprintf(__VA_ARGS__)
^
estimateExpression.cpp:301:97: warning: implicit conversion changes signedness: 'long' to 'size_type' (aka 'unsigned long') [-Wsign-conversion]
message(" %7.4lf (%7.4lf | %6ld | %7.4lf)",rH1,rH2,rHat2[i].SS-1,totAverage[rHat2[i].SS].FF);
˜˜˜˜˜ ^
./common.h:17:30: note: expanded from macro 'message'
#define message(...) Rprintf(__VA_ARGS__)
^
estimateExpression.cpp:311:53: warning: implicit conversion changes signedness: 'long' to 'size_type' (aka 'unsigned long') [-Wsign-conversion]
for(j=0;j<chainsN;j++)message("%ld ",samplers[j]->getAverageC0());
˜˜˜˜˜˜˜˜ ^
./common.h:17:30: note: expanded from macro 'message'
#define message(...) Rprintf(__VA_ARGS__)
^
estimateExpression.cpp:323:42: warning: implicit conversion changes signedness: 'long' to 'size_type' (aka 'unsigned long') [-Wsign-conversion]
for(i=0;(i<M) && (sqrt(rHat2[i].FF.FF) > gPar.targetScaleReduction());i++){
˜˜˜˜˜ ^
estimateExpression.cpp:324:28: warning: implicit conversion changes signedness: 'long' to 'size_type' (aka 'unsigned long') [-Wsign-conversion]
sstr<<rHat2[i].SS<<" ("<<sqrt(rHat2[i].FF.FF)<<") ";
˜˜˜˜˜ ^
estimateExpression.cpp:324:52: warning: implicit conversion changes signedness: 'long' to 'size_type' (aka 'unsigned long') [-Wsign-conversion]
sstr<<rHat2[i].SS<<" ("<<sqrt(rHat2[i].FF.FF)<<") ";
˜˜˜˜˜ ^
estimateExpression.cpp:325:68: warning: implicit conversion changes signedness: 'long' to 'size_type' (aka 'unsigned long') [-Wsign-conversion]
message(" %s( %ld , %lf )\n",(trInfo.trName(rHat2[i].SS-1)).c_str(),rHat2[i].SS-1,sqrt(rHat2[i].FF.FF));
˜˜˜˜˜ ^
./common.h:17:30: note: expanded from macro 'message'
#define message(...) Rprintf(__VA_ARGS__)
^
estimateExpression.cpp:325:92: warning: implicit conversion changes signedness: 'long' to 'size_type' (aka 'unsigned long') [-Wsign-conversion]
message(" %s( %ld , %lf )\n",(trInfo.trName(rHat2[i].SS-1)).c_str(),rHat2[i].SS-1,sqrt(rHat2[i].FF.FF));
˜˜˜˜˜ ^
./common.h:17:30: note: expanded from macro 'message'
#define message(...) Rprintf(__VA_ARGS__)
^
estimateExpression.cpp:325:111: warning: implicit conversion changes signedness: 'long' to 'size_type' (aka 'unsigned long') [-Wsign-conversion]
message(" %s( %ld , %lf )\n",(trInfo.trName(rHat2[i].SS-1)).c_str(),rHat2[i].SS-1,sqrt(rHat2[i].FF.FF));
˜˜˜˜˜ ^
./common.h:17:30: note: expanded from macro 'message'
#define message(...) Rprintf(__VA_ARGS__)
^
estimateExpression.cpp:331:22: warning: implicit conversion changes signedness: 'long' to 'size_type' (aka 'unsigned long') [-Wsign-conversion]
samplers[j]->noSave();
˜˜˜˜˜˜˜˜ ^
estimateExpression.cpp:337:31: warning: implicit conversion changes signedness: 'long' to 'size_type' (aka 'unsigned long') [-Wsign-conversion]
vector<double> needS(M,0);
˜˜˜˜˜ ^
estimateExpression.cpp:341:19: warning: implicit conversion changes signedness: 'long' to 'size_type' (aka 'unsigned long') [-Wsign-conversion]
needS[i] = samplesSave * samplesHave/
˜˜˜˜˜ ^
estimateExpression.cpp:342:61: warning: implicit conversion changes signedness: 'long' to 'size_type' (aka 'unsigned long') [-Wsign-conversion]
((samplesHave-1.0)/samplesHave*withVar[i].FF/betwVar[i].FF+1.0);
˜˜˜˜˜˜˜ ^
estimateExpression.cpp:342:75: warning: implicit conversion changes signedness: 'long' to 'size_type' (aka 'unsigned long') [-Wsign-conversion]
((samplesHave-1.0)/samplesHave*withVar[i].FF/betwVar[i].FF+1.0);
˜˜˜˜˜˜˜ ^
estimateExpression.cpp:357:37: warning: implicit conversion changes signedness: 'long' to 'size_type' (aka 'unsigned long') [-Wsign-conversion]
samplesN = max((long)needS[i],samplesSave);
˜˜˜˜˜ ^
estimateExpression.cpp:383:50: warning: implicit conversion changes signedness: 'long' to 'size_type' (aka 'unsigned long') [-Wsign-conversion]
samplesFile[j].open(samplesFileNames[j].c_str());
˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜ ^
estimateExpression.cpp:388:25: warning: implicit conversion changes signedness: 'long' to 'size_type' (aka 'unsigned long') [-Wsign-conversion]
samplers[j]->saveSamples(&samplesFile[j],trInfo.getShiftedLengths(true),outTypeI);
˜˜˜˜˜˜˜˜ ^
estimateExpression.cpp:393:19: warning: implicit conversion changes signedness: 'long' to 'size_type' (aka 'unsigned long') [-Wsign-conversion]
samplers[j]->resetSampler(samplesN);
˜˜˜˜˜˜˜˜ ^
estimateExpression.cpp:414:27: warning: implicit conversion changes signedness: 'long' to 'size_type' (aka 'unsigned long') [-Wsign-conversion]
sum+=samplers[j]->getAverage(i).FF;
˜˜˜˜˜˜˜˜ ^
estimateExpression.cpp:415:28: warning: implicit conversion changes signedness: 'long' to 'size_type' (aka 'unsigned long') [-Wsign-conversion]
sum2+=samplers[j]->getAverage(i).SS;
˜˜˜˜˜˜˜˜ ^
estimateExpression.cpp:424:38: warning: implicit conversion changes signedness: 'long' to 'size_type' (aka 'unsigned long') [-Wsign-conversion]
meansFile<<" "<<samplers[j]->getAverage(i).FF;
˜˜˜˜˜˜˜˜ ^
estimateExpression.cpp:439:38: warning: implicit conversion changes signedness: 'long' to 'size_type' (aka 'unsigned long') [-Wsign-conversion]
for(i=0;i<(long)samplers[j]->getThetaActLog().size();i++)
˜˜˜˜˜˜˜˜ ^
estimateExpression.cpp:440:34: warning: implicit conversion changes signedness: 'long' to 'size_type' (aka 'unsigned long') [-Wsign-conversion]
actFile<<samplers[j]->getThetaActLog()[i]<<" ";
˜˜˜˜˜˜˜˜ ^
estimateExpression.cpp:440:55: warning: implicit conversion changes signedness: 'long' to 'size_type' (aka 'unsigned long') [-Wsign-conversion]
actFile<<samplers[j]->getThetaActLog()[i]<<" ";
˜˜˜˜˜˜˜˜ ^
estimateExpression.cpp:451:23: warning: implicit conversion changes signedness: 'long' to 'size_type' (aka 'unsigned long') [-Wsign-conversion]
delete samplers[j];
˜˜˜˜˜˜˜˜ ^
estimateExpression.cpp:550:34: warning: implicit conversion changes signedness: 'long' to 'size_type' (aka 'unsigned long') [-Wsign-conversion]
remove(samplesFileNames[i].c_str());
˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜ ^
93 warnings generated.
clang++ -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -DPACKAGE_NAME=\"Bitseq\" -DPACKAGE_TARNAME=\"bitseq\" -DPACKAGE_VERSION=\"1.4.x\" -DPACKAGE_STRING=\"Bitseq\ 1.4.x\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DBS_VERSION=\"1.4.2\" -DBIOC_BUILD=1 -D_USE_KNETFILE -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -I/usr/local/include -I"/Library/Frameworks/R.framework/Versions/3.0/Resources/library/Rsamtools/include" -I"/Library/Frameworks/R.framework/Versions/3.0/Resources/library/zlibbioc/include" -I. -fPIC -mtune=native -g -O2 -Wall -pedantic -Wconversion -c estimateHyperPar.cpp -o estimateHyperPar.o
In file included from estimateHyperPar.cpp:10:
In file included from ./boost/random/mersenne_twister.hpp:29:
In file included from ./boost/random/detail/seed_impl.hpp:27:
In file included from ./boost/random/detail/const_mod.hpp:23:
./boost/random/detail/large_arithmetic.hpp:94:14: warning: implicit conversion changes signedness: 'int' to 'unsigned int' [-Wsign-conversion]
q -= error;
˜˜ ^˜˜˜˜
./boost/random/detail/large_arithmetic.hpp:95:21: warning: implicit conversion changes signedness: 'int' to 'unsigned long' [-Wsign-conversion]
rem = rem + error * m - diff;
^˜˜˜˜ ˜
In file included from estimateHyperPar.cpp:10:
./boost/random/mersenne_twister.hpp:493:14: warning: 'long long' is a C++11 extension [-Wc++11-long-long]
UINT64_C(0xb5026f5aa96619e9),29,UINT64_C(0x5555555555555555),17,
^
/usr/include/stdint.h:248:23: note: expanded from macro 'UINT64_C'
#define UINT64_C(v) (v ## ULL)
^
<scratch space>:92:1: note: expanded from macro '0xb5026f5aa96619e9'
0xb5026f5aa96619e9ULL
^
In file included from estimateHyperPar.cpp:10:
./boost/random/mersenne_twister.hpp:493:46: warning: 'long long' is a C++11 extension [-Wc++11-long-long]
UINT64_C(0xb5026f5aa96619e9),29,UINT64_C(0x5555555555555555),17,
^
/usr/include/stdint.h:248:23: note: expanded from macro 'UINT64_C'
#define UINT64_C(v) (v ## ULL)
^
<scratch space>:92:1: note: expanded from macro '0x5555555555555555'
0x5555555555555555ULL
^
In file included from estimateHyperPar.cpp:10:
./boost/random/mersenne_twister.hpp:494:14: warning: 'long long' is a C++11 extension [-Wc++11-long-long]
UINT64_C(0x71d67fffeda60000),37,UINT64_C(0xfff7eee000000000),43,
^
/usr/include/stdint.h:248:23: note: expanded from macro 'UINT64_C'
#define UINT64_C(v) (v ## ULL)
^
<scratch space>:92:1: note: expanded from macro '0x71d67fffeda60000'
0x71d67fffeda60000ULL
^
In file included from estimateHyperPar.cpp:10:
./boost/random/mersenne_twister.hpp:494:46: warning: 'long long' is a C++11 extension [-Wc++11-long-long]
UINT64_C(0x71d67fffeda60000),37,UINT64_C(0xfff7eee000000000),43,
^
/usr/include/stdint.h:248:23: note: expanded from macro 'UINT64_C'
#define UINT64_C(v) (v ## ULL)
^
<scratch space>:92:1: note: expanded from macro '0xfff7eee000000000'
0xfff7eee000000000ULL
^
In file included from estimateHyperPar.cpp:10:
./boost/random/mersenne_twister.hpp:495:14: warning: 'long long' is a C++11 extension [-Wc++11-long-long]
UINT64_C(6364136223846793005)> mt19937_64;
^
/usr/include/stdint.h:248:23: note: expanded from macro 'UINT64_C'
#define UINT64_C(v) (v ## ULL)
^
<scratch space>:92:1: note: expanded from macro '6364136223846793005'
6364136223846793005ULL
^
In file included from estimateHyperPar.cpp:16:
./common.h:17:17: warning: variadic macros are a C99 feature [-Wvariadic-macros]
#define message(...) Rprintf(__VA_ARGS__)
^
In file included from estimateHyperPar.cpp:18:
./MyTimer.h:28:20: warning: implicit conversion changes signedness: 'long' to 'size_type' (aka 'unsigned long') [-Wsign-conversion]
times.resize(N);
˜˜˜˜˜ ^
./MyTimer.h:36:23: warning: implicit conversion changes signedness: 'long' to 'size_type' (aka 'unsigned long') [-Wsign-conversion]
times.resize(N);
˜˜˜˜˜ ^
./MyTimer.h:38:13: warning: implicit conversion changes signedness: 'long' to 'size_type' (aka 'unsigned long') [-Wsign-conversion]
times[timer]=time(NULL);
˜˜˜˜˜ ^˜˜˜˜
./MyTimer.h:43:28: warning: implicit conversion changes signedness: 'long' to 'size_type' (aka 'unsigned long') [-Wsign-conversion]
ret=time(NULL)-times[timer];
˜˜˜˜˜ ^˜˜˜˜
./MyTimer.h:46:13: warning: implicit conversion changes signedness: 'long' to 'size_type' (aka 'unsigned long') [-Wsign-conversion]
times[timer]=time(NULL);
˜˜˜˜˜ ^˜˜˜˜
./MyTimer.h:52:28: warning: implicit conversion changes signedness: 'long' to 'size_type' (aka 'unsigned long') [-Wsign-conversion]
ret=time(NULL)-times[timer];
˜˜˜˜˜ ^˜˜˜˜
./MyTimer.h:60:28: warning: implicit conversion changes signedness: 'long' to 'size_type' (aka 'unsigned long') [-Wsign-conversion]
ret=time(NULL)-times[timer];
˜˜˜˜˜ ^˜˜˜˜
./MyTimer.h:63:13: warning: implicit conversion changes signedness: 'long' to 'size_type' (aka 'unsigned long') [-Wsign-conversion]
times[timer]=time(NULL);
˜˜˜˜˜ ^˜˜˜˜
In file included from estimateHyperPar.cpp:21:
./TranscriptExpression.h:32:38: warning: implicit conversion changes signedness: 'long' to 'size_type' (aka 'unsigned long') [-Wsign-conversion]
double exp(long tr){return trs[tr].exp;}
˜˜˜ ^˜
./TranscriptExpression.h:33:38: warning: implicit conversion changes signedness: 'long' to 'size_type' (aka 'unsigned long') [-Wsign-conversion]
double var(long tr){return trs[tr].var;}
˜˜˜ ^˜
./TranscriptExpression.h:34:35: warning: implicit conversion changes signedness: 'long' to 'size_type' (aka 'unsigned long') [-Wsign-conversion]
long id(long tr){return trs[tr].id;}
˜˜˜ ^˜
estimateHyperPar.cpp:112:76: warning: implicit conversion changes signedness: 'long' to 'size_type' (aka 'unsigned long') [-Wsign-conversion]
vector<vector<vector<double> > > tr(subM_MAX,vector<vector<double> >(RTN));
˜˜˜˜˜˜ ^˜˜
estimateHyperPar.cpp:113:71: warning: implicit conversion changes signedness: 'long' to 'size_type' (aka 'unsigned long') [-Wsign-conversion]
vector<vector<long double> > bAdd(subM_MAX,vector<long double> (C,0));
˜˜˜˜˜˜ ^
estimateHyperPar.cpp:148:64: warning: implicit conversion changes signedness: 'long' to 'size_type' (aka 'unsigned long') [-Wsign-conversion]
good = cond.getTranscript(r, trExp.id(curM), tr[m][r],samplesN+MAX_RETRIES);
˜˜ ^
estimateHyperPar.cpp:148:67: warning: implicit conversion changes signedness: 'long' to 'size_type' (aka 'unsigned long') [-Wsign-conversion]
good = cond.getTranscript(r, trExp.id(curM), tr[m][r],samplesN+MAX_RETRIES);
˜˜ ^
estimateHyperPar.cpp:153:25: warning: implicit conversion changes signedness: 'long' to 'size_type' (aka 'unsigned long') [-Wsign-conversion]
tr[m][r][samp] = (tr[m][r][samp] == 0)? ns_misc::LOG_ZERO:log(tr[m][r][samp]);
˜˜ ^
estimateHyperPar.cpp:153:28: warning: implicit conversion changes signedness: 'long' to 'size_type' (aka 'unsigned long') [-Wsign-conversion]
tr[m][r][samp] = (tr[m][r][samp] == 0)? ns_misc::LOG_ZERO:log(tr[m][r][samp]);
˜˜ ^
estimateHyperPar.cpp:153:31: warning: implicit conversion changes signedness: 'long' to 'size_type' (aka 'unsigned long') [-Wsign-conversion]
tr[m][r][samp] = (tr[m][r][samp] == 0)? ns_misc::LOG_ZERO:log(tr[m][r][samp]);
˜˜ ^˜˜˜
estimateHyperPar.cpp:153:43: warning: implicit conversion changes signedness: 'long' to 'size_type' (aka 'unsigned long') [-Wsign-conversion]
tr[m][r][samp] = (tr[m][r][samp] == 0)? ns_misc::LOG_ZERO:log(tr[m][r][samp]);
˜˜ ^
estimateHyperPar.cpp:153:46: warning: implicit conversion changes signedness: 'long' to 'size_type' (aka 'unsigned long') [-Wsign-conversion]
tr[m][r][samp] = (tr[m][r][samp] == 0)? ns_misc::LOG_ZERO:log(tr[m][r][samp]);
˜˜ ^
estimateHyperPar.cpp:153:49: warning: implicit conversion changes signedness: 'long' to 'size_type' (aka 'unsigned long') [-Wsign-conversion]
tr[m][r][samp] = (tr[m][r][samp] == 0)? ns_misc::LOG_ZERO:log(tr[m][r][samp]);
˜˜ ^˜˜˜
estimateHyperPar.cpp:153:87: warning: implicit conversion changes signedness: 'long' to 'size_type' (aka 'unsigned long') [-Wsign-conversion]
tr[m][r][samp] = (tr[m][r][samp] == 0)? ns_misc::LOG_ZERO:log(tr[m][r][samp]);
˜˜ ^
estimateHyperPar.cpp:153:90: warning: implicit conversion changes signedness: 'long' to 'size_type' (aka 'unsigned long') [-Wsign-conversion]
tr[m][r][samp] = (tr[m][r][samp] == 0)? ns_misc::LOG_ZERO:log(tr[m][r][samp]);
˜˜ ^
estimateHyperPar.cpp:153:93: warning: implicit conversion changes signedness: 'long' to 'size_type' (aka 'unsigned long') [-Wsign-conversion]
tr[m][r][samp] = (tr[m][r][samp] == 0)? ns_misc::LOG_ZERO:log(tr[m][r][samp]);
˜˜ ^˜˜˜
estimateHyperPar.cpp:157:20: warning: implicit conversion changes signedness: 'long' to 'size_type' (aka 'unsigned long') [-Wsign-conversion]
mu0[m]=trExp.exp(curM);
˜˜˜ ^
estimateHyperPar.cpp:158:26: warning: implicit conversion changes signedness: 'long' to 'size_type' (aka 'unsigned long') [-Wsign-conversion]
mean+=mu0[m];
˜˜˜ ^
estimateHyperPar.cpp:182:32: warning: implicit conversion changes signedness: 'long' to 'size_type' (aka 'unsigned long') [-Wsign-conversion]
sum += tr[m][i][samp];
˜˜ ^
estimateHyperPar.cpp:182:35: warning: implicit conversion changes signedness: 'long' to 'size_type' (aka 'unsigned long') [-Wsign-conversion]
sum += tr[m][i][samp];
˜˜ ^
estimateHyperPar.cpp:182:38: warning: implicit conversion changes signedness: 'long' to 'size_type' (aka 'unsigned long') [-Wsign-conversion]
sum += tr[m][i][samp];
˜˜ ^˜˜˜
estimateHyperPar.cpp:183:33: warning: implicit conversion changes signedness: 'long' to 'size_type' (aka 'unsigned long') [-Wsign-conversion]
sumS += tr[m][i][samp]*tr[m][i][samp];
˜˜ ^
estimateHyperPar.cpp:183:36: warning: implicit conversion changes signedness: 'long' to 'size_type' (aka 'unsigned long') [-Wsign-conversion]
sumS += tr[m][i][samp]*tr[m][i][samp];
˜˜ ^
estimateHyperPar.cpp:183:39: warning: implicit conversion changes signedness: 'long' to 'size_type' (aka 'unsigned long') [-Wsign-conversion]
sumS += tr[m][i][samp]*tr[m][i][samp];
˜˜ ^˜˜˜
estimateHyperPar.cpp:183:48: warning: implicit conversion changes signedness: 'long' to 'size_type' (aka 'unsigned long') [-Wsign-conversion]
sumS += tr[m][i][samp]*tr[m][i][samp];
˜˜ ^
estimateHyperPar.cpp:183:51: warning: implicit conversion changes signedness: 'long' to 'size_type' (aka 'unsigned long') [-Wsign-conversion]
sumS += tr[m][i][samp]*tr[m][i][samp];
˜˜ ^
estimateHyperPar.cpp:183:54: warning: implicit conversion changes signedness: 'long' to 'size_type' (aka 'unsigned long') [-Wsign-conversion]
sumS += tr[m][i][samp]*tr[m][i][samp];
˜˜ ^˜˜˜
estimateHyperPar.cpp:186:24: warning: implicit conversion changes signedness: 'long' to 'size_type' (aka 'unsigned long') [-Wsign-conversion]
bAdd[m][c]=0.5*(sumS + mu0[m]*mu0[m]*lambda0 -
˜˜˜˜ ^
estimateHyperPar.cpp:186:27: warning: implicit conversion changes signedness: 'long' to 'size_type' (aka 'unsigned long') [-Wsign-conversion]
bAdd[m][c]=0.5*(sumS + mu0[m]*mu0[m]*lambda0 -
˜˜˜˜ ^
estimateHyperPar.cpp:186:46: warning: implicit conversion changes signedness: 'long' to 'size_type' (aka 'unsigned long') [-Wsign-conversion]
bAdd[m][c]=0.5*(sumS + mu0[m]*mu0[m]*lambda0 -
˜˜˜ ^
estimateHyperPar.cpp:186:53: warning: implicit conversion changes signedness: 'long' to 'size_type' (aka 'unsigned long') [-Wsign-conversion]
bAdd[m][c]=0.5*(sumS + mu0[m]*mu0[m]*lambda0 -
˜˜˜ ^
estimateHyperPar.cpp:187:34: warning: implicit conversion changes signedness: 'long' to 'size_type' (aka 'unsigned long') [-Wsign-conversion]
(sum+mu0[m]*lambda0)*(sum+mu0[m]*lambda0)/(lambda0+Rc));
˜˜˜ ^
estimateHyperPar.cpp:187:55: warning: implicit conversion changes signedness: 'long' to 'size_type' (aka 'unsigned long') [-Wsign-conversion]
(sum+mu0[m]*lambda0)*(sum+mu0[m]*lambda0)/(lambda0+Rc));
˜˜˜ ^
estimateHyperPar.cpp:239:47: warning: implicit conversion loses floating-point precision: 'long double' to 'double' [-Wconversion]
probC = lgamma(alphaP + cond.getRC(c)/2.0)+
˜˜˜˜˜˜ ˜˜˜˜˜˜˜^˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜
estimateHyperPar.cpp:240:36: warning: implicit conversion loses floating-point precision: 'long double' to 'double' [-Wconversion]
lgamma(alpha) -
˜˜˜˜˜˜ ^˜˜˜˜
estimateHyperPar.cpp:241:42: warning: implicit conversion loses floating-point precision: 'long double' to 'double' [-Wconversion]
lgamma(alpha + cond.getRC(c)/2.0) -
˜˜˜˜˜˜ ˜˜˜˜˜˜^˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜
estimateHyperPar.cpp:242:36: warning: implicit conversion loses floating-point precision: 'long double' to 'double' [-Wconversion]
lgamma(alphaP);
˜˜˜˜˜˜ ^˜˜˜˜˜
estimateHyperPar.cpp:247:50: warning: implicit conversion changes signedness: 'long' to 'size_type' (aka 'unsigned long') [-Wsign-conversion]
prob *= pow(beta+bAdd[m][c], alpha) /
˜˜˜˜ ^
estimateHyperPar.cpp:247:53: warning: implicit conversion changes signedness: 'long' to 'size_type' (aka 'unsigned long') [-Wsign-conversion]
prob *= pow(beta+bAdd[m][c], alpha) /
˜˜˜˜ ^
estimateHyperPar.cpp:248:51: warning: implicit conversion changes signedness: 'long' to 'size_type' (aka 'unsigned long') [-Wsign-conversion]
pow(betaP+bAdd[m][c], alphaP);
˜˜˜˜ ^
estimateHyperPar.cpp:248:54: warning: implicit conversion changes signedness: 'long' to 'size_type' (aka 'unsigned long') [-Wsign-conversion]
pow(betaP+bAdd[m][c], alphaP);
˜˜˜˜ ^
estimateHyperPar.cpp:249:52: warning: implicit conversion changes signedness: 'long' to 'size_type' (aka 'unsigned long') [-Wsign-conversion]
prob *= pow( (beta+bAdd[m][c])/(betaP+bAdd[m][c]), (long double)(cond.getRC(c)/2.0));
˜˜˜˜ ^
estimateHyperPar.cpp:249:55: warning: implicit conversion changes signedness: 'long' to 'size_type' (aka 'unsigned long') [-Wsign-conversion]
prob *= pow( (beta+bAdd[m][c])/(betaP+bAdd[m][c]), (long double)(cond.getRC(c)/2.0));
˜˜˜˜ ^
estimateHyperPar.cpp:249:71: warning: implicit conversion changes signedness: 'long' to 'size_type' (aka 'unsigned long') [-Wsign-conversion]
prob *= pow( (beta+bAdd[m][c])/(betaP+bAdd[m][c]), (long double)(cond.getRC(c)/2.0));
˜˜˜˜ ^
estimateHyperPar.cpp:249:74: warning: implicit conversion changes signedness: 'long' to 'size_type' (aka 'unsigned long') [-Wsign-conversion]
prob *= pow( (beta+bAdd[m][c])/(betaP+bAdd[m][c]), (long double)(cond.getRC(c)/2.0));
˜˜˜˜ ^
estimateHyperPar.cpp:267:27: warning: implicit conversion loses floating-point precision: 'long double' to 'double' [-Wconversion]
param.expr=mean;
˜^˜˜˜
estimateHyperPar.cpp:268:28: warning: implicit conversion loses floating-point precision: 'long double' to 'double' [-Wconversion]
param.alpha=alpha;
˜^˜˜˜˜
estimateHyperPar.cpp:269:27: warning: implicit conversion loses floating-point precision: 'long double' to 'double' [-Wconversion]
param.beta=beta;
˜^˜˜˜
estimateHyperPar.cpp:300:23: warning: implicit conversion changes signedness: 'long' to 'size_type' (aka 'unsigned long') [-Wsign-conversion]
vector<double> exp(pAll),alp(pAll),bet(pAll),alpS,betS;
˜˜˜ ^˜˜˜
estimateHyperPar.cpp:300:33: warning: implicit conversion changes signedness: 'long' to 'size_type' (aka 'unsigned long') [-Wsign-conversion]
vector<double> exp(pAll),alp(pAll),bet(pAll),alpS,betS;
˜˜˜ ^˜˜˜
estimateHyperPar.cpp:300:43: warning: implicit conversion changes signedness: 'long' to 'size_type' (aka 'unsigned long') [-Wsign-conversion]
vector<double> exp(pAll),alp(pAll),bet(pAll),alpS,betS;
˜˜˜ ^˜˜˜
estimateHyperPar.cpp:302:11: warning: implicit conversion changes signedness: 'long' to 'size_type' (aka 'unsigned long') [-Wsign-conversion]
exp[i]=params[i].expr;
˜˜˜ ^
estimateHyperPar.cpp:302:21: warning: implicit conversion changes signedness: 'long' to 'size_type' (aka 'unsigned long') [-Wsign-conversion]
exp[i]=params[i].expr;
˜˜˜˜˜˜ ^
estimateHyperPar.cpp:303:11: warning: implicit conversion changes signedness: 'long' to 'size_type' (aka 'unsigned long') [-Wsign-conversion]
alp[i]=params[i].alpha;
˜˜˜ ^
estimateHyperPar.cpp:303:21: warning: implicit conversion changes signedness: 'long' to 'size_type' (aka 'unsigned long') [-Wsign-conversion]
alp[i]=params[i].alpha;
˜˜˜˜˜˜ ^
estimateHyperPar.cpp:304:11: warning: implicit conversion changes signedness: 'long' to 'size_type' (aka 'unsigned long') [-Wsign-conversion]
bet[i]=params[i].beta;
˜˜˜ ^
estimateHyperPar.cpp:304:21: warning: implicit conversion changes signedness: 'long' to 'size_type' (aka 'unsigned long') [-Wsign-conversion]
bet[i]=params[i].beta;
˜˜˜˜˜˜ ^
estimateHyperPar.cpp:313:18: warning: implicit conversion changes signedness: 'long' to 'size_type' (aka 'unsigned long') [-Wsign-conversion]
if(alpS[i]<=0){
˜˜˜˜ ^
estimateHyperPar.cpp:315:88: warning: implicit conversion changes signedness: 'long' to 'size_type' (aka 'unsigned long') [-Wsign-conversion]
if(args.flag("veryVerbose"))message(" negative alpha: %lg exp: %lg\n",alpS[i],exp[i]);
˜˜˜˜ ^
./common.h:17:30: note: expanded from macro 'message'
#define message(...) Rprintf(__VA_ARGS__)
^
estimateHyperPar.cpp:315:95: warning: implicit conversion changes signedness: 'long' to 'size_type' (aka 'unsigned long') [-Wsign-conversion]
if(args.flag("veryVerbose"))message(" negative alpha: %lg exp: %lg\n",alpS[i],exp[i]);
˜˜˜ ^
./common.h:17:30: note: expanded from macro 'message'
#define message(...) Rprintf(__VA_ARGS__)
^
estimateHyperPar.cpp:332:18: warning: implicit conversion changes signedness: 'long' to 'size_type' (aka 'unsigned long') [-Wsign-conversion]
if(betS[i]<=0){
˜˜˜˜ ^
estimateHyperPar.cpp:334:87: warning: implicit conversion changes signedness: 'long' to 'size_type' (aka 'unsigned long') [-Wsign-conversion]
if(args.flag("veryVerbose"))message(" negative beta: %lg exp: %lg\n",betS[i],exp[i]);
˜˜˜˜ ^
./common.h:17:30: note: expanded from macro 'message'
#define message(...) Rprintf(__VA_ARGS__)
^
estimateHyperPar.cpp:334:94: warning: implicit conversion changes signedness: 'long' to 'size_type' (aka 'unsigned long') [-Wsign-conversion]
if(args.flag("veryVerbose"))message(" negative beta: %lg exp: %lg\n",betS[i],exp[i]);
˜˜˜ ^
./common.h:17:30: note: expanded from macro 'message'
#define message(...) Rprintf(__VA_ARGS__)
^
estimateHyperPar.cpp:349:33: warning: implicit conversion changes signedness: 'long' to 'size_type' (aka 'unsigned long') [-Wsign-conversion]
while((i<pAll)&&((alpS[i]<=0)||(betS[i]<=0))){
˜˜˜˜ ^
estimateHyperPar.cpp:349:47: warning: implicit conversion changes signedness: 'long' to 'size_type' (aka 'unsigned long') [-Wsign-conversion]
while((i<pAll)&&((alpS[i]<=0)||(betS[i]<=0))){
˜˜˜˜ ^
estimateHyperPar.cpp:350:52: warning: implicit conversion changes signedness: 'long' to 'size_type' (aka 'unsigned long') [-Wsign-conversion]
message("Removing: %lg %lg %lg\n",alpS[i],betS[i],exp[i]);
˜˜˜˜ ^
./common.h:17:30: note: expanded from macro 'message'
#define message(...) Rprintf(__VA_ARGS__)
^
estimateHyperPar.cpp:350:60: warning: implicit conversion changes signedness: 'long' to 'size_type' (aka 'unsigned long') [-Wsign-conversion]
message("Removing: %lg %lg %lg\n",alpS[i],betS[i],exp[i]);
˜˜˜˜ ^
./common.h:17:30: note: expanded from macro 'message'
#define message(...) Rprintf(__VA_ARGS__)
^
estimateHyperPar.cpp:350:67: warning: implicit conversion changes signedness: 'long' to 'size_type' (aka 'unsigned long') [-Wsign-conversion]
message("Removing: %lg %lg %lg\n",alpS[i],betS[i],exp[i]);
˜˜˜ ^
./common.h:17:30: note: expanded from macro 'message'
#define message(...) Rprintf(__VA_ARGS__)
^
estimateHyperPar.cpp:352:20: warning: implicit conversion changes signedness: 'size_type' (aka 'unsigned long') to 'long' [-Wsign-conversion]
pAll = alpS.size();
˜ ^˜˜˜˜˜˜˜˜˜˜
estimateHyperPar.cpp:356:30: warning: implicit conversion changes signedness: 'long' to 'size_type' (aka 'unsigned long') [-Wsign-conversion]
for(i=1;i<pAll;i++)if(exp[i]!=exp[i-1])pDistinct++;
˜˜˜ ^
estimateHyperPar.cpp:356:39: warning: implicit conversion changes signedness: 'long' to 'size_type' (aka 'unsigned long') [-Wsign-conversion]
for(i=1;i<pAll;i++)if(exp[i]!=exp[i-1])pDistinct++;
˜˜˜ ˜^˜
estimateHyperPar.cpp:361:14: warning: implicit conversion changes signedness: 'long' to 'size_type' (aka 'unsigned long') [-Wsign-conversion]
if(exp[i]!=exp[i-1])outF<<alpS[i]<<" "<<betS[i]<<" "<<exp[i]<<endl;
˜˜˜ ^
estimateHyperPar.cpp:361:23: warning: implicit conversion changes signedness: 'long' to 'size_type' (aka 'unsigned long') [-Wsign-conversion]
if(exp[i]!=exp[i-1])outF<<alpS[i]<<" "<<betS[i]<<" "<<exp[i]<<endl;
˜˜˜ ˜^˜
estimateHyperPar.cpp:361:38: warning: implicit conversion changes signedness: 'long' to 'size_type' (aka 'unsigned long') [-Wsign-conversion]
if(exp[i]!=exp[i-1])outF<<alpS[i]<<" "<<betS[i]<<" "<<exp[i]<<endl;
˜˜˜˜ ^
estimateHyperPar.cpp:361:52: warning: implicit conversion changes signedness: 'long' to 'size_type' (aka 'unsigned long') [-Wsign-conversion]
if(exp[i]!=exp[i-1])outF<<alpS[i]<<" "<<betS[i]<<" "<<exp[i]<<endl;
˜˜˜˜ ^
estimateHyperPar.cpp:361:65: warning: implicit conversion changes signedness: 'long' to 'size_type' (aka 'unsigned long') [-Wsign-conversion]
if(exp[i]!=exp[i-1])outF<<alpS[i]<<" "<<betS[i]<<" "<<exp[i]<<endl;
˜˜˜ ^
estimateHyperPar.cpp:114:38: warning: implicit conversion loses integer precision: 'long' to 'const unsigned int' [-Wshorten-64-to-32]
boost::random::mt11213b rng_mt(ns_misc::getSeed(args));
˜˜˜˜˜˜ ^˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜
93 warnings generated.
clang++ -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -DPACKAGE_NAME=\"Bitseq\" -DPACKAGE_TARNAME=\"bitseq\" -DPACKAGE_VERSION=\"1.4.x\" -DPACKAGE_STRING=\"Bitseq\ 1.4.x\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DBS_VERSION=\"1.4.2\" -DBIOC_BUILD=1 -D_USE_KNETFILE -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -I/usr/local/include -I"/Library/Frameworks/R.framework/Versions/3.0/Resources/library/Rsamtools/include" -I"/Library/Frameworks/R.framework/Versions/3.0/Resources/library/zlibbioc/include" -I. -fPIC -mtune=native -g -O2 -Wall -pedantic -Wconversion -c getGeneExpression.cpp -o getGeneExpression.o
In file included from getGeneExpression.cpp:11:
./common.h:17:17: warning: variadic macros are a C99 feature [-Wvariadic-macros]
#define message(...) Rprintf(__VA_ARGS__)
^
getGeneExpression.cpp:50:32: warning: implicit conversion changes signedness: 'long' to 'size_type' (aka 'unsigned long') [-Wsign-conversion]
vector<long double> normals(N,0);
˜˜˜˜˜˜˜ ^
getGeneExpression.cpp:54:25: warning: implicit conversion changes signedness: 'long' to 'size_type' (aka 'unsigned long') [-Wsign-conversion]
vector<double> tr(M);
˜˜ ^
getGeneExpression.cpp:60:21: warning: implicit conversion changes signedness: 'long' to 'size_type' (aka 'unsigned long') [-Wsign-conversion]
normals[i] += tr[i]/trInfo.L(j);
˜˜˜˜˜˜˜ ^
getGeneExpression.cpp:60:30: warning: implicit conversion changes signedness: 'long' to 'size_type' (aka 'unsigned long') [-Wsign-conversion]
normals[i] += tr[i]/trInfo.L(j);
˜˜ ^
getGeneExpression.cpp:66:12: warning: implicit conversion changes signedness: 'size_type' (aka 'unsigned long') to 'long' [-Wsign-conversion]
gM = trInfo.getGtrs(g)->size();
˜ ^˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜
getGeneExpression.cpp:67:41: warning: implicit conversion changes signedness: 'long' to 'size_type' (aka 'unsigned long') [-Wsign-conversion]
if((long)trs.size()<gM)trs.resize(gM);
˜˜˜ ^˜
getGeneExpression.cpp:70:35: warning: implicit conversion changes signedness: 'long' to 'size_type' (aka 'unsigned long') [-Wsign-conversion]
m = (*trInfo.getGtrs(g))[j];
˜ ^
getGeneExpression.cpp:71:41: warning: implicit conversion changes signedness: 'long' to 'size_type' (aka 'unsigned long') [-Wsign-conversion]
samples.getTranscript( m , trs[j]);
˜˜˜ ^
getGeneExpression.cpp:76:35: warning: implicit conversion changes signedness: 'long' to 'size_type' (aka 'unsigned long') [-Wsign-conversion]
if(doAdjust&&(normals[i]>0)){
˜˜˜˜˜˜˜ ^
getGeneExpression.cpp:77:41: warning: implicit conversion changes signedness: 'long' to 'size_type' (aka 'unsigned long') [-Wsign-conversion]
m = (*trInfo.getGtrs(g))[j];
˜ ^
getGeneExpression.cpp:78:26: warning: implicit conversion changes signedness: 'long' to 'size_type' (aka 'unsigned long') [-Wsign-conversion]
sum+=(trs[j][i] / trInfo.L(m)) / normals[i];
˜˜˜ ^
getGeneExpression.cpp:78:29: warning: implicit conversion changes signedness: 'long' to 'size_type' (aka 'unsigned long') [-Wsign-conversion]
sum+=(trs[j][i] / trInfo.L(m)) / normals[i];
˜˜˜ ^
getGeneExpression.cpp:78:57: warning: implicit conversion changes signedness: 'long' to 'size_type' (aka 'unsigned long') [-Wsign-conversion]
sum+=(trs[j][i] / trInfo.L(m)) / normals[i];
˜˜˜˜˜˜˜ ^
getGeneExpression.cpp:80:25: warning: implicit conversion changes signedness: 'long' to 'size_type' (aka 'unsigned long') [-Wsign-conversion]
sum+=trs[j][i];
˜˜˜ ^
getGeneExpression.cpp:80:28: warning: implicit conversion changes signedness: 'long' to 'size_type' (aka 'unsigned long') [-Wsign-conversion]
sum+=trs[j][i];
˜˜˜ ^
16 warnings generated.
clang++ -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -DPACKAGE_NAME=\"Bitseq\" -DPACKAGE_TARNAME=\"bitseq\" -DPACKAGE_VERSION=\"1.4.x\" -DPACKAGE_STRING=\"Bitseq\ 1.4.x\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DBS_VERSION=\"1.4.2\" -DBIOC_BUILD=1 -D_USE_KNETFILE -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -I/usr/local/include -I"/Library/Frameworks/R.framework/Versions/3.0/Resources/library/Rsamtools/include" -I"/Library/Frameworks/R.framework/Versions/3.0/Resources/library/zlibbioc/include" -I. -fPIC -mtune=native -g -O2 -Wall -pedantic -Wconversion -c getVariance.cpp -o getVariance.o
In file included from getVariance.cpp:13:
./common.h:17:17: warning: variadic macros are a C99 feature [-Wvariadic-macros]
#define message(...) Rprintf(__VA_ARGS__)
^
getVariance.cpp:50:25: warning: implicit conversion changes signedness: 'long' to 'size_type' (aka 'unsigned long') [-Wsign-conversion]
while(args.args()[i]=="C")i++;
˜˜˜˜ ^
getVariance.cpp:51:46: warning: implicit conversion changes signedness: 'long' to 'size_type' (aka 'unsigned long') [-Wsign-conversion]
message("using only: %s ",(args.args()[i]).c_str());
˜˜˜˜ ^
./common.h:17:30: note: expanded from macro 'message'
#define message(...) Rprintf(__VA_ARGS__)
^
getVariance.cpp:53:25: warning: implicit conversion changes signedness: 'long' to 'size_type' (aka 'unsigned long') [-Wsign-conversion]
while(args.args()[i]=="C")i++;
˜˜˜˜ ^
getVariance.cpp:54:35: warning: implicit conversion changes signedness: 'long' to 'size_type' (aka 'unsigned long') [-Wsign-conversion]
message("%s\n",(args.args()[i]).c_str());
˜˜˜˜ ^
./common.h:17:30: note: expanded from macro 'message'
#define message(...) Rprintf(__VA_ARGS__)
^
getVariance.cpp:63:24: warning: implicit conversion changes signedness: 'long' to 'size_type' (aka 'unsigned long') [-Wsign-conversion]
vector<double> mean(M),var(M);
˜˜˜˜ ^
getVariance.cpp:63:31: warning: implicit conversion changes signedness: 'long' to 'size_type' (aka 'unsigned long') [-Wsign-conversion]
vector<double> mean(M),var(M);
˜˜˜ ^
getVariance.cpp:76:25: warning: implicit conversion changes signedness: 'long' to 'size_type' (aka 'unsigned long') [-Wsign-conversion]
tr[i]=tr[i]<=0?LOG_ZERO:log(tr[i]);
˜˜ ^
getVariance.cpp:76:31: warning: implicit conversion changes signedness: 'long' to 'size_type' (aka 'unsigned long') [-Wsign-conversion]
tr[i]=tr[i]<=0?LOG_ZERO:log(tr[i]);
˜˜ ^
getVariance.cpp:76:53: warning: implicit conversion changes signedness: 'long' to 'size_type' (aka 'unsigned long') [-Wsign-conversion]
tr[i]=tr[i]<=0?LOG_ZERO:log(tr[i]);
˜˜ ^
getVariance.cpp:78:25: warning: implicit conversion changes signedness: 'long' to 'size_type' (aka 'unsigned long') [-Wsign-conversion]
m+=tr[i];
˜˜ ^
getVariance.cpp:79:29: warning: implicit conversion changes signedness: 'long' to 'size_type' (aka 'unsigned long') [-Wsign-conversion]
mSq += tr[i]*tr[i];
˜˜ ^
getVariance.cpp:79:35: warning: implicit conversion changes signedness: 'long' to 'size_type' (aka 'unsigned long') [-Wsign-conversion]
mSq += tr[i]*tr[i];
˜˜ ^
getVariance.cpp:90:18: warning: implicit conversion changes signedness: 'long' to 'size_type' (aka 'unsigned long') [-Wsign-conversion]
mean[j] = -47;
˜˜˜˜ ^
getVariance.cpp:91:17: warning: implicit conversion changes signedness: 'long' to 'size_type' (aka 'unsigned long') [-Wsign-conversion]
var[j] = -47;
˜˜˜ ^
getVariance.cpp:93:18: warning: implicit conversion changes signedness: 'long' to 'size_type' (aka 'unsigned long') [-Wsign-conversion]
mean[j] = m / count;
˜˜˜˜ ^
getVariance.cpp:94:17: warning: implicit conversion changes signedness: 'long' to 'size_type' (aka 'unsigned long') [-Wsign-conversion]
var[j] = mSq/count - m*m/(count*count);
˜˜˜ ^
getVariance.cpp:103:21: warning: implicit conversion changes signedness: 'long' to 'size_type' (aka 'unsigned long') [-Wsign-conversion]
mean[j] = -47;
˜˜˜˜ ^
getVariance.cpp:104:20: warning: implicit conversion changes signedness: 'long' to 'size_type' (aka 'unsigned long') [-Wsign-conversion]
var[j] = -47;
˜˜˜ ^
getVariance.cpp:108:25: warning: implicit conversion changes signedness: 'long' to 'size_type' (aka 'unsigned long') [-Wsign-conversion]
tr2.resize(N/2);
˜˜˜ ˜^˜
getVariance.cpp:110:20: warning: implicit conversion changes signedness: 'long' to 'size_type' (aka 'unsigned long') [-Wsign-conversion]
tr2[i]=tr[i+N/2];
˜˜˜ ^
getVariance.cpp:110:27: warning: implicit conversion changes signedness: 'long' to 'size_type' (aka 'unsigned long') [-Wsign-conversion]
tr2[i]=tr[i+N/2];
˜˜ ˜^˜˜˜
getVariance.cpp:114:21: warning: implicit conversion changes signedness: 'long' to 'size_type' (aka 'unsigned long') [-Wsign-conversion]
mean[j] = -47;
˜˜˜˜ ^
getVariance.cpp:115:20: warning: implicit conversion changes signedness: 'long' to 'size_type' (aka 'unsigned long') [-Wsign-conversion]
var[j] = -47;
˜˜˜ ^
getVariance.cpp:123:22: warning: implicit conversion changes signedness: 'long' to 'size_type' (aka 'unsigned long') [-Wsign-conversion]
tr[i]=log(tr[i]);
˜˜ ^
getVariance.cpp:123:32: warning: implicit conversion changes signedness: 'long' to 'size_type' (aka 'unsigned long') [-Wsign-conversion]
tr[i]=log(tr[i]);
˜˜ ^
getVariance.cpp:124:23: warning: implicit conversion changes signedness: 'long' to 'size_type' (aka 'unsigned long') [-Wsign-conversion]
tr2[i]=log(tr2[i]);
˜˜˜ ^
getVariance.cpp:124:34: warning: implicit conversion changes signedness: 'long' to 'size_type' (aka 'unsigned long') [-Wsign-conversion]
tr2[i]=log(tr2[i]);
˜˜˜ ^
getVariance.cpp:126:22: warning: implicit conversion changes signedness: 'long' to 'size_type' (aka 'unsigned long') [-Wsign-conversion]
m+=tr[i]+tr2[i];
˜˜ ^
getVariance.cpp:126:29: warning: implicit conversion changes signedness: 'long' to 'size_type' (aka 'unsigned long') [-Wsign-conversion]
m+=tr[i]+tr2[i];
˜˜˜ ^
getVariance.cpp:127:27: warning: implicit conversion changes signedness: 'long' to 'size_type' (aka 'unsigned long') [-Wsign-conversion]
sqDif+=(tr[i]-tr2[i])*(tr[i]-tr2[i]);
˜˜ ^
getVariance.cpp:127:34: warning: implicit conversion changes signedness: 'long' to 'size_type' (aka 'unsigned long') [-Wsign-conversion]
sqDif+=(tr[i]-tr2[i])*(tr[i]-tr2[i]);
˜˜˜ ^
getVariance.cpp:127:42: warning: implicit conversion changes signedness: 'long' to 'size_type' (aka 'unsigned long') [-Wsign-conversion]
sqDif+=(tr[i]-tr2[i])*(tr[i]-tr2[i]);
˜˜ ^
getVariance.cpp:127:49: warning: implicit conversion changes signedness: 'long' to 'size_type' (aka 'unsigned long') [-Wsign-conversion]
sqDif+=(tr[i]-tr2[i])*(tr[i]-tr2[i]);
˜˜˜ ^
getVariance.cpp:129:18: warning: implicit conversion changes signedness: 'long' to 'size_type' (aka 'unsigned long') [-Wsign-conversion]
mean[j] = m / N;
˜˜˜˜ ^
getVariance.cpp:130:17: warning: implicit conversion changes signedness: 'long' to 'size_type' (aka 'unsigned long') [-Wsign-conversion]
var[j] = sqDif / N; // == ( sqDif / (N/2) ) / 2
˜˜˜ ^
getVariance.cpp:138:42: warning: implicit conversion changes signedness: 'long' to 'size_type' (aka 'unsigned long') [-Wsign-conversion]
for(r=0;r<RN;r++)outFile<<args.args()[r]<<" ";
˜˜˜˜ ^
getVariance.cpp:144:16: warning: implicit conversion changes signedness: 'long' to 'size_type' (aka 'unsigned long') [-Wsign-conversion]
if((mean[i]==-47)&&(var[i]==-47))outFile<<"NaN 0 "<<endl;
˜˜˜˜ ^
getVariance.cpp:144:31: warning: implicit conversion changes signedness: 'long' to 'size_type' (aka 'unsigned long') [-Wsign-conversion]
if((mean[i]==-47)&&(var[i]==-47))outFile<<"NaN 0 "<<endl;
˜˜˜ ^
getVariance.cpp:145:26: warning: implicit conversion changes signedness: 'long' to 'size_type' (aka 'unsigned long') [-Wsign-conversion]
else outFile<<mean[i]<<" "<<var[i]<<endl;
˜˜˜˜ ^
getVariance.cpp:145:39: warning: implicit conversion changes signedness: 'long' to 'size_type' (aka 'unsigned long') [-Wsign-conversion]
else outFile<<mean[i]<<" "<<var[i]<<endl;
˜˜˜ ^
41 warnings generated.
clang++ -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -DPACKAGE_NAME=\"Bitseq\" -DPACKAGE_TARNAME=\"bitseq\" -DPACKAGE_VERSION=\"1.4.x\" -DPACKAGE_STRING=\"Bitseq\ 1.4.x\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DBS_VERSION=\"1.4.2\" -DBIOC_BUILD=1 -D_USE_KNETFILE -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -I/usr/local/include -I"/Library/Frameworks/R.framework/Versions/3.0/Resources/library/Rsamtools/include" -I"/Library/Frameworks/R.framework/Versions/3.0/Resources/library/zlibbioc/include" -I. -fPIC -mtune=native -g -O2 -Wall -pedantic -Wconversion -c getWithinGeneExpression.cpp -o getWithinGeneExpression.o
In file included from getWithinGeneExpression.cpp:11:
./common.h:17:17: warning: variadic macros are a C99 feature [-Wvariadic-macros]
#define message(...) Rprintf(__VA_ARGS__)
^
getWithinGeneExpression.cpp:63:29: warning: implicit conversion changes signedness: 'long' to 'size_type' (aka 'unsigned long') [-Wsign-conversion]
vector<long double> mean(M),mean2(M),sqSum(M),sqSum2(M);
˜˜˜˜ ^
getWithinGeneExpression.cpp:63:38: warning: implicit conversion changes signedness: 'long' to 'size_type' (aka 'unsigned long') [-Wsign-conversion]
vector<long double> mean(M),mean2(M),sqSum(M),sqSum2(M);
˜˜˜˜˜ ^
getWithinGeneExpression.cpp:63:47: warning: implicit conversion changes signedness: 'long' to 'size_type' (aka 'unsigned long') [-Wsign-conversion]
vector<long double> mean(M),mean2(M),sqSum(M),sqSum2(M);
˜˜˜˜˜ ^
getWithinGeneExpression.cpp:63:57: warning: implicit conversion changes signedness: 'long' to 'size_type' (aka 'unsigned long') [-Wsign-conversion]
vector<long double> mean(M),mean2(M),sqSum(M),sqSum2(M);
˜˜˜˜˜˜ ^
getWithinGeneExpression.cpp:65:32: warning: implicit conversion changes signedness: 'long' to 'size_type' (aka 'unsigned long') [-Wsign-conversion]
vector<long double> normals(N,0);
˜˜˜˜˜˜˜ ^
getWithinGeneExpression.cpp:69:25: warning: implicit conversion changes signedness: 'long' to 'size_type' (aka 'unsigned long') [-Wsign-conversion]
vector<double> tr(M);
˜˜ ^
getWithinGeneExpression.cpp:75:21: warning: implicit conversion changes signedness: 'long' to 'size_type' (aka 'unsigned long') [-Wsign-conversion]
normals[i] += tr[i]/trInfo.L(j);
˜˜˜˜˜˜˜ ^
getWithinGeneExpression.cpp:75:30: warning: implicit conversion changes signedness: 'long' to 'size_type' (aka 'unsigned long') [-Wsign-conversion]
normals[i] += tr[i]/trInfo.L(j);
˜˜ ^
getWithinGeneExpression.cpp:81:12: warning: implicit conversion changes signedness: 'size_type' (aka 'unsigned long') to 'long' [-Wsign-conversion]
gM = trInfo.getGtrs(g)->size();
˜ ^˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜
getWithinGeneExpression.cpp:82:41: warning: implicit conversion changes signedness: 'long' to 'size_type' (aka 'unsigned long') [-Wsign-conversion]
if((long)trs.size()<gM)trs.resize(gM);
˜˜˜ ^˜
getWithinGeneExpression.cpp:85:35: warning: implicit conversion changes signedness: 'long' to 'size_type' (aka 'unsigned long') [-Wsign-conversion]
m = (*trInfo.getGtrs(g))[j];
˜ ^
getWithinGeneExpression.cpp:86:41: warning: implicit conversion changes signedness: 'long' to 'size_type' (aka 'unsigned long') [-Wsign-conversion]
samples.getTranscript( m , trs[j]);
˜˜˜ ^
getWithinGeneExpression.cpp:87:15: warning: implicit conversion changes signedness: 'long' to 'size_type' (aka 'unsigned long') [-Wsign-conversion]
mean[m] = mean2[m] = sqSum[m] = sqSum2[m] = 0;
˜˜˜˜ ^
getWithinGeneExpression.cpp:87:26: warning: implicit conversion changes signedness: 'long' to 'size_type' (aka 'unsigned long') [-Wsign-conversion]
mean[m] = mean2[m] = sqSum[m] = sqSum2[m] = 0;
˜˜˜˜˜ ^
getWithinGeneExpression.cpp:87:37: warning: implicit conversion changes signedness: 'long' to 'size_type' (aka 'unsigned long') [-Wsign-conversion]
mean[m] = mean2[m] = sqSum[m] = sqSum2[m] = 0;
˜˜˜˜˜ ^
getWithinGeneExpression.cpp:87:49: warning: implicit conversion changes signedness: 'long' to 'size_type' (aka 'unsigned long') [-Wsign-conversion]
mean[m] = mean2[m] = sqSum[m] = sqSum2[m] = 0;
˜˜˜˜˜˜ ^
getWithinGeneExpression.cpp:93:41: warning: implicit conversion changes signedness: 'long' to 'size_type' (aka 'unsigned long') [-Wsign-conversion]
m = (*trInfo.getGtrs(g))[j];
˜ ^
getWithinGeneExpression.cpp:95:20: warning: implicit conversion changes signedness: 'long' to 'size_type' (aka 'unsigned long') [-Wsign-conversion]
trs[j][i]/=l;
˜˜˜ ^
getWithinGeneExpression.cpp:95:23: warning: implicit conversion changes signedness: 'long' to 'size_type' (aka 'unsigned long') [-Wsign-conversion]
trs[j][i]/=l;
˜˜˜ ^
getWithinGeneExpression.cpp:96:27: warning: implicit conversion changes signedness: 'long' to 'size_type' (aka 'unsigned long') [-Wsign-conversion]
if(normals[i]!=0)trs[j][i]/=normals[i];
˜˜˜˜˜˜˜ ^
getWithinGeneExpression.cpp:96:37: warning: implicit conversion changes signedness: 'long' to 'size_type' (aka 'unsigned long') [-Wsign-conversion]
if(normals[i]!=0)trs[j][i]/=normals[i];
˜˜˜ ^
getWithinGeneExpression.cpp:96:40: warning: implicit conversion changes signedness: 'long' to 'size_type' (aka 'unsigned long') [-Wsign-conversion]
if(normals[i]!=0)trs[j][i]/=normals[i];
˜˜˜ ^
getWithinGeneExpression.cpp:96:52: warning: implicit conversion changes signedness: 'long' to 'size_type' (aka 'unsigned long') [-Wsign-conversion]
if(normals[i]!=0)trs[j][i]/=normals[i];
˜˜˜˜˜˜˜ ^
getWithinGeneExpression.cpp:98:19: warning: implicit conversion changes signedness: 'long' to 'size_type' (aka 'unsigned long') [-Wsign-conversion]
x=trs[j][i];
˜˜˜ ^
getWithinGeneExpression.cpp:98:22: warning: implicit conversion changes signedness: 'long' to 'size_type' (aka 'unsigned long') [-Wsign-conversion]
x=trs[j][i];
˜˜˜ ^
getWithinGeneExpression.cpp:101:41: warning: implicit conversion changes signedness: 'long' to 'size_type' (aka 'unsigned long') [-Wsign-conversion]
m = (*trInfo.getGtrs(g))[j];
˜ ^
getWithinGeneExpression.cpp:102:35: warning: implicit conversion changes signedness: 'long' to 'size_type' (aka 'unsigned long') [-Wsign-conversion]
if(doLog)x=log(trs[j][i]);
˜˜˜ ^
getWithinGeneExpression.cpp:102:38: warning: implicit conversion changes signedness: 'long' to 'size_type' (aka 'unsigned long') [-Wsign-conversion]
if(doLog)x=log(trs[j][i]);
˜˜˜ ^
getWithinGeneExpression.cpp:103:21: warning: implicit conversion changes signedness: 'long' to 'size_type' (aka 'unsigned long') [-Wsign-conversion]
mean[m] += x;
˜˜˜˜ ^
getWithinGeneExpression.cpp:104:22: warning: implicit conversion changes signedness: 'long' to 'size_type' (aka 'unsigned long') [-Wsign-conversion]
sqSum[m] += x*x;
˜˜˜˜˜ ^
getWithinGeneExpression.cpp:108:17: warning: implicit conversion changes signedness: 'long' to 'size_type' (aka 'unsigned long') [-Wsign-conversion]
trs[j][i] /= sum;
˜˜˜ ^
getWithinGeneExpression.cpp:108:20: warning: implicit conversion changes signedness: 'long' to 'size_type' (aka 'unsigned long') [-Wsign-conversion]
trs[j][i] /= sum;
˜˜˜ ^
getWithinGeneExpression.cpp:109:26: warning: implicit conversion changes signedness: 'long' to 'size_type' (aka 'unsigned long') [-Wsign-conversion]
if(doLog)trs[j][i] = log(trs[j][i]);
˜˜˜ ^
getWithinGeneExpression.cpp:109:29: warning: implicit conversion changes signedness: 'long' to 'size_type' (aka 'unsigned long') [-Wsign-conversion]
if(doLog)trs[j][i] = log(trs[j][i]);
˜˜˜ ^
getWithinGeneExpression.cpp:109:42: warning: implicit conversion changes signedness: 'long' to 'size_type' (aka 'unsigned long') [-Wsign-conversion]
if(doLog)trs[j][i] = log(trs[j][i]);
˜˜˜ ^
getWithinGeneExpression.cpp:109:45: warning: implicit conversion changes signedness: 'long' to 'size_type' (aka 'unsigned long') [-Wsign-conversion]
if(doLog)trs[j][i] = log(trs[j][i]);
˜˜˜ ^
getWithinGeneExpression.cpp:111:41: warning: implicit conversion changes signedness: 'long' to 'size_type' (aka 'unsigned long') [-Wsign-conversion]
m = (*trInfo.getGtrs(g))[j];
˜ ^
getWithinGeneExpression.cpp:112:22: warning: implicit conversion changes signedness: 'long' to 'size_type' (aka 'unsigned long') [-Wsign-conversion]
mean2[m] += trs[j][i];
˜˜˜˜˜ ^
getWithinGeneExpression.cpp:112:32: warning: implicit conversion changes signedness: 'long' to 'size_type' (aka 'unsigned long') [-Wsign-conversion]
mean2[m] += trs[j][i];
˜˜˜ ^
getWithinGeneExpression.cpp:112:35: warning: implicit conversion changes signedness: 'long' to 'size_type' (aka 'unsigned long') [-Wsign-conversion]
mean2[m] += trs[j][i];
˜˜˜ ^
getWithinGeneExpression.cpp:113:23: warning: implicit conversion changes signedness: 'long' to 'size_type' (aka 'unsigned long') [-Wsign-conversion]
sqSum2[m] += trs[j][i]*trs[j][i];
˜˜˜˜˜˜ ^
getWithinGeneExpression.cpp:113:33: warning: implicit conversion changes signedness: 'long' to 'size_type' (aka 'unsigned long') [-Wsign-conversion]
sqSum2[m] += trs[j][i]*trs[j][i];
˜˜˜ ^
getWithinGeneExpression.cpp:113:36: warning: implicit conversion changes signedness: 'long' to 'size_type' (aka 'unsigned long') [-Wsign-conversion]
sqSum2[m] += trs[j][i]*trs[j][i];
˜˜˜ ^
getWithinGeneExpression.cpp:113:43: warning: implicit conversion changes signedness: 'long' to 'size_type' (aka 'unsigned long') [-Wsign-conversion]
sqSum2[m] += trs[j][i]*trs[j][i];
˜˜˜ ^
getWithinGeneExpression.cpp:113:46: warning: implicit conversion changes signedness: 'long' to 'size_type' (aka 'unsigned long') [-Wsign-conversion]
sqSum2[m] += trs[j][i]*trs[j][i];
˜˜˜ ^
getWithinGeneExpression.cpp:120:29: warning: implicit conversion changes signedness: 'long' to 'size_type' (aka 'unsigned long') [-Wsign-conversion]
outFile<<trs[j][i]<<" ";
˜˜˜ ^
getWithinGeneExpression.cpp:120:32: warning: implicit conversion changes signedness: 'long' to 'size_type' (aka 'unsigned long') [-Wsign-conversion]
outFile<<trs[j][i]<<" ";
˜˜˜ ^
getWithinGeneExpression.cpp:128:15: warning: implicit conversion changes signedness: 'long' to 'size_type' (aka 'unsigned long') [-Wsign-conversion]
mean[j] /= N;
˜˜˜˜ ^
getWithinGeneExpression.cpp:129:22: warning: implicit conversion changes signedness: 'long' to 'size_type' (aka 'unsigned long') [-Wsign-conversion]
var = sqSum[j]/N - mean[j]*mean[j];
˜˜˜˜˜ ^
getWithinGeneExpression.cpp:129:34: warning: implicit conversion changes signedness: 'long' to 'size_type' (aka 'unsigned long') [-Wsign-conversion]
var = sqSum[j]/N - mean[j]*mean[j];
˜˜˜˜ ^
getWithinGeneExpression.cpp:129:42: warning: implicit conversion changes signedness: 'long' to 'size_type' (aka 'unsigned long') [-Wsign-conversion]
var = sqSum[j]/N - mean[j]*mean[j];
˜˜˜˜ ^
getWithinGeneExpression.cpp:130:16: warning: implicit conversion changes signedness: 'long' to 'size_type' (aka 'unsigned long') [-Wsign-conversion]
mean2[j] /= N;
˜˜˜˜˜ ^
getWithinGeneExpression.cpp:131:24: warning: implicit conversion changes signedness: 'long' to 'size_type' (aka 'unsigned long') [-Wsign-conversion]
var2 = sqSum2[j]/N - mean2[j]*mean2[j];
˜˜˜˜˜˜ ^
getWithinGeneExpression.cpp:131:37: warning: implicit conversion changes signedness: 'long' to 'size_type' (aka 'unsigned long') [-Wsign-conversion]
var2 = sqSum2[j]/N - mean2[j]*mean2[j];
˜˜˜˜˜ ^
getWithinGeneExpression.cpp:131:46: warning: implicit conversion changes signedness: 'long' to 'size_type' (aka 'unsigned long') [-Wsign-conversion]
var2 = sqSum2[j]/N - mean2[j]*mean2[j];
˜˜˜˜˜ ^
getWithinGeneExpression.cpp:132:24: warning: implicit conversion changes signedness: 'long' to 'size_type' (aka 'unsigned long') [-Wsign-conversion]
sumFile<<mean[j]<<" "<<var<<" "<<mean2[j]<<" "<<var2<<endl;
˜˜˜˜ ^
getWithinGeneExpression.cpp:132:49: warning: implicit conversion changes signedness: 'long' to 'size_type' (aka 'unsigned long') [-Wsign-conversion]
sumFile<<mean[j]<<" "<<var<<" "<<mean2[j]<<" "<<var2<<endl;
˜˜˜˜˜ ^
58 warnings generated.
clang++ -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -DPACKAGE_NAME=\"Bitseq\" -DPACKAGE_TARNAME=\"bitseq\" -DPACKAGE_VERSION=\"1.4.x\" -DPACKAGE_STRING=\"Bitseq\ 1.4.x\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DBS_VERSION=\"1.4.2\" -DBIOC_BUILD=1 -D_USE_KNETFILE -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -I/usr/local/include -I"/Library/Frameworks/R.framework/Versions/3.0/Resources/library/Rsamtools/include" -I"/Library/Frameworks/R.framework/Versions/3.0/Resources/library/zlibbioc/include" -I. -fPIC -mtune=native -g -O2 -Wall -pedantic -Wconversion -c lowess.cpp -o lowess.o
In file included from lowess.cpp:24:
./common.h:17:17: warning: variadic macros are a C99 feature [-Wvariadic-macros]
#define message(...) Rprintf(__VA_ARGS__)
^
lowess.cpp:36:14: warning: implicit conversion changes signedness: 'long' to 'size_type' (aka 'unsigned long') [-Wsign-conversion]
ys.resize(n);
˜˜ ^
lowess.cpp:37:14: warning: implicit conversion changes signedness: 'long' to 'size_type' (aka 'unsigned long') [-Wsign-conversion]
rw.resize(n);
˜˜ ^
lowess.cpp:38:15: warning: implicit conversion changes signedness: 'long' to 'size_type' (aka 'unsigned long') [-Wsign-conversion]
res.resize(n);
˜˜˜ ^
lowess.cpp:56:20: warning: implicit conversion changes signedness: 'long' to 'size_type' (aka 'unsigned long') [-Wsign-conversion]
d1 = x[i]-x[nleft];
˜ ^
lowess.cpp:56:25: warning: implicit conversion changes signedness: 'long' to 'size_type' (aka 'unsigned long') [-Wsign-conversion]
d1 = x[i]-x[nleft];
˜ ^˜˜˜˜
lowess.cpp:57:26: warning: implicit conversion changes signedness: 'long' to 'size_type' (aka 'unsigned long') [-Wsign-conversion]
d2 = x[nright+1] - x[i];
˜ ˜˜˜˜˜˜^˜
lowess.cpp:57:34: warning: implicit conversion changes signedness: 'long' to 'size_type' (aka 'unsigned long') [-Wsign-conversion]
d2 = x[nright+1] - x[i];
˜ ^
lowess.cpp:63:23: warning: implicit conversion changes signedness: 'long' to 'size_type' (aka 'unsigned long') [-Wsign-conversion]
lowest(x,y,x[i],ys[i],nleft,nright,res,iter>0,rw,ok);
˜ ^
lowess.cpp:63:29: warning: implicit conversion changes signedness: 'long' to 'size_type' (aka 'unsigned long') [-Wsign-conversion]
lowest(x,y,x[i],ys[i],nleft,nright,res,iter>0,rw,ok);
˜˜ ^
lowess.cpp:64:21: warning: implicit conversion changes signedness: 'long' to 'size_type' (aka 'unsigned long') [-Wsign-conversion]
if(!ok) ys[i]=y[i];
˜˜ ^
lowess.cpp:64:26: warning: implicit conversion changes signedness: 'long' to 'size_type' (aka 'unsigned long') [-Wsign-conversion]
if(!ok) ys[i]=y[i];
˜ ^
lowess.cpp:70:23: warning: implicit conversion changes signedness: 'long' to 'size_type' (aka 'unsigned long') [-Wsign-conversion]
denom = x[i] - x[last];
˜ ^
lowess.cpp:70:30: warning: implicit conversion changes signedness: 'long' to 'size_type' (aka 'unsigned long') [-Wsign-conversion]
denom = x[i] - x[last];
˜ ^˜˜˜
lowess.cpp:72:27: warning: implicit conversion changes signedness: 'long' to 'size_type' (aka 'unsigned long') [-Wsign-conversion]
alpha = (x[j]-x[last])/denom;
˜ ^
lowess.cpp:72:32: warning: implicit conversion changes signedness: 'long' to 'size_type' (aka 'unsigned long') [-Wsign-conversion]
alpha = (x[j]-x[last])/denom;
˜ ^˜˜˜
lowess.cpp:73:19: warning: implicit conversion changes signedness: 'long' to 'size_type' (aka 'unsigned long') [-Wsign-conversion]
ys[j] = alpha * ys[i] + (1.0-alpha)*ys[last];
˜˜ ^
lowess.cpp:73:35: warning: implicit conversion changes signedness: 'long' to 'size_type' (aka 'unsigned long') [-Wsign-conversion]
ys[j] = alpha * ys[i] + (1.0-alpha)*ys[last];
˜˜ ^
lowess.cpp:73:55: warning: implicit conversion changes signedness: 'long' to 'size_type' (aka 'unsigned long') [-Wsign-conversion]
ys[j] = alpha * ys[i] + (1.0-alpha)*ys[last];
˜˜ ^˜˜˜
lowess.cpp:77:18: warning: implicit conversion changes signedness: 'long' to 'size_type' (aka 'unsigned long') [-Wsign-conversion]
cut = x[last]+delta;
˜ ^˜˜˜
lowess.cpp:79:18: warning: implicit conversion changes signedness: 'long' to 'size_type' (aka 'unsigned long') [-Wsign-conversion]
if(x[i]>cut)break;
˜ ^
lowess.cpp:80:18: warning: implicit conversion changes signedness: 'long' to 'size_type' (aka 'unsigned long') [-Wsign-conversion]
if(x[i]==x[last]){
˜ ^
lowess.cpp:80:24: warning: implicit conversion changes signedness: 'long' to 'size_type' (aka 'unsigned long') [-Wsign-conversion]
if(x[i]==x[last]){
˜ ^˜˜˜
lowess.cpp:81:19: warning: implicit conversion changes signedness: 'long' to 'size_type' (aka 'unsigned long') [-Wsign-conversion]
ys[i]=ys[last];
˜˜ ^
lowess.cpp:81:25: warning: implicit conversion changes signedness: 'long' to 'size_type' (aka 'unsigned long') [-Wsign-conversion]
ys[i]=ys[last];
˜˜ ^˜˜˜
lowess.cpp:88:14: warning: implicit conversion changes signedness: 'long' to 'size_type' (aka 'unsigned long') [-Wsign-conversion]
res[i] = y[i]-ys[i];
˜˜˜ ^
lowess.cpp:88:21: warning: implicit conversion changes signedness: 'long' to 'size_type' (aka 'unsigned long') [-Wsign-conversion]
res[i] = y[i]-ys[i];
˜ ^
lowess.cpp:88:27: warning: implicit conversion changes signedness: 'long' to 'size_type' (aka 'unsigned long') [-Wsign-conversion]
res[i] = y[i]-ys[i];
˜˜ ^
lowess.cpp:91:13: warning: implicit conversion changes signedness: 'long' to 'size_type' (aka 'unsigned long') [-Wsign-conversion]
rw[i]=abs(res[i]);
˜˜ ^
lowess.cpp:91:24: warning: implicit conversion changes signedness: 'long' to 'size_type' (aka 'unsigned long') [-Wsign-conversion]
rw[i]=abs(res[i]);
˜˜˜ ^
lowess.cpp:96:23: warning: implicit conversion changes signedness: 'long' to 'size_type' (aka 'unsigned long') [-Wsign-conversion]
cmad = 3.0 *(rw[m1]+rw[m2]);
˜˜ ^˜
lowess.cpp:96:30: warning: implicit conversion changes signedness: 'long' to 'size_type' (aka 'unsigned long') [-Wsign-conversion]
cmad = 3.0 *(rw[m1]+rw[m2]);
˜˜ ^˜
lowess.cpp:100:22: warning: implicit conversion changes signedness: 'long' to 'size_type' (aka 'unsigned long') [-Wsign-conversion]
r = abs(res[i]);
˜˜˜ ^
lowess.cpp:101:23: warning: implicit conversion changes signedness: 'long' to 'size_type' (aka 'unsigned long') [-Wsign-conversion]
if(r<=c1) rw[i]=1;
˜˜ ^
lowess.cpp:102:27: warning: implicit conversion changes signedness: 'long' to 'size_type' (aka 'unsigned long') [-Wsign-conversion]
else if(r>c9) rw[i]=0;
˜˜ ^
lowess.cpp:103:18: warning: implicit conversion changes signedness: 'long' to 'size_type' (aka 'unsigned long') [-Wsign-conversion]
else rw[i] = (1.0-(r/cmad)*(r/cmad))*(1.0-(r/cmad)*(r/cmad));
˜˜ ^
lowess.cpp:112:15: warning: implicit conversion changes signedness: 'long' to 'size_type' (aka 'unsigned long') [-Wsign-conversion]
range = x[n-1]-x[0];
˜ ˜^˜
lowess.cpp:113:17: warning: implicit conversion changes signedness: 'long' to 'size_type' (aka 'unsigned long') [-Wsign-conversion]
h = max(xs-x[nleft],x[nright]-xs);
˜ ^˜˜˜˜
lowess.cpp:113:26: warning: implicit conversion changes signedness: 'long' to 'size_type' (aka 'unsigned long') [-Wsign-conversion]
h = max(xs-x[nleft],x[nright]-xs);
˜ ^˜˜˜˜˜
lowess.cpp:120:9: warning: implicit conversion changes signedness: 'long' to 'size_type' (aka 'unsigned long') [-Wsign-conversion]
w[j]=0.;
˜ ^
lowess.cpp:121:17: warning: implicit conversion changes signedness: 'long' to 'size_type' (aka 'unsigned long') [-Wsign-conversion]
r = abs(x[j]-xs);
˜ ^
lowess.cpp:124:21: warning: implicit conversion changes signedness: 'long' to 'size_type' (aka 'unsigned long') [-Wsign-conversion]
if(r>h1) w[j] = (1.0-(r/h)*(r/h)*(r/h))*(1.0-(r/h)*(r/h)*(r/h))*(1.0-(r/h)*(r/h)*(r/h));
˜ ^
lowess.cpp:125:17: warning: implicit conversion changes signedness: 'long' to 'size_type' (aka 'unsigned long') [-Wsign-conversion]
else w[j] = 1.;
˜ ^
lowess.cpp:126:22: warning: implicit conversion changes signedness: 'long' to 'size_type' (aka 'unsigned long') [-Wsign-conversion]
if(userw) w[j] *= rw[j];
˜ ^
lowess.cpp:126:31: warning: implicit conversion changes signedness: 'long' to 'size_type' (aka 'unsigned long') [-Wsign-conversion]
if(userw) w[j] *= rw[j];
˜˜ ^
lowess.cpp:127:17: warning: implicit conversion changes signedness: 'long' to 'size_type' (aka 'unsigned long') [-Wsign-conversion]
a += w[j];
˜ ^
lowess.cpp:128:18: warning: implicit conversion changes signedness: 'long' to 'size_type' (aka 'unsigned long') [-Wsign-conversion]
}else if(x[j]>xs) break; // get out at first zero wt on right
˜ ^
lowess.cpp:138:12: warning: implicit conversion changes signedness: 'long' to 'size_type' (aka 'unsigned long') [-Wsign-conversion]
w[j] /= a;
˜ ^
lowess.cpp:143:20: warning: implicit conversion changes signedness: 'long' to 'size_type' (aka 'unsigned long') [-Wsign-conversion]
a += w[j]*x[j]; // weighted centre of values
˜ ^
lowess.cpp:143:25: warning: implicit conversion changes signedness: 'long' to 'size_type' (aka 'unsigned long') [-Wsign-conversion]
a += w[j]*x[j]; // weighted centre of values
˜ ^
lowess.cpp:147:20: warning: implicit conversion changes signedness: 'long' to 'size_type' (aka 'unsigned long') [-Wsign-conversion]
c += w[j]*(x[j]-a)*(x[j]-a);
˜ ^
lowess.cpp:147:26: warning: implicit conversion changes signedness: 'long' to 'size_type' (aka 'unsigned long') [-Wsign-conversion]
c += w[j]*(x[j]-a)*(x[j]-a);
˜ ^
lowess.cpp:147:35: warning: implicit conversion changes signedness: 'long' to 'size_type' (aka 'unsigned long') [-Wsign-conversion]
c += w[j]*(x[j]-a)*(x[j]-a);
˜ ^
lowess.cpp:152:18: warning: implicit conversion changes signedness: 'long' to 'size_type' (aka 'unsigned long') [-Wsign-conversion]
w[j] *= (1.0+b*(x[j]-a));
˜ ^
lowess.cpp:152:34: warning: implicit conversion changes signedness: 'long' to 'size_type' (aka 'unsigned long') [-Wsign-conversion]
w[j] *= (1.0+b*(x[j]-a));
˜ ^
lowess.cpp:157:18: warning: implicit conversion changes signedness: 'long' to 'size_type' (aka 'unsigned long') [-Wsign-conversion]
ys += w[j]*y[j];
˜ ^
lowess.cpp:157:23: warning: implicit conversion changes signedness: 'long' to 'size_type' (aka 'unsigned long') [-Wsign-conversion]
ys += w[j]*y[j];
˜ ^
57 warnings generated.
clang++ -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -DPACKAGE_NAME=\"Bitseq\" -DPACKAGE_TARNAME=\"bitseq\" -DPACKAGE_VERSION=\"1.4.x\" -DPACKAGE_STRING=\"Bitseq\ 1.4.x\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DBS_VERSION=\"1.4.2\" -DBIOC_BUILD=1 -D_USE_KNETFILE -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -I/usr/local/include -I"/Library/Frameworks/R.framework/Versions/3.0/Resources/library/Rsamtools/include" -I"/Library/Frameworks/R.framework/Versions/3.0/Resources/library/zlibbioc/include" -I. -fPIC -mtune=native -g -O2 -Wall -pedantic -Wconversion -c misc.cpp -o misc.o
In file included from misc.cpp:6:
./common.h:17:17: warning: variadic macros are a C99 feature [-Wvariadic-macros]
#define message(...) Rprintf(__VA_ARGS__)
^
misc.cpp:19:52: warning: implicit conversion changes signedness: 'size_type' (aka 'unsigned long') to 'long' [-Wsign-conversion]
if((en == -1) || (en > (long)vals.size())) en = vals.size();
˜ ^˜˜˜˜˜˜˜˜˜˜
misc.cpp:23:24: warning: implicit conversion changes signedness: 'long' to 'size_type' (aka 'unsigned long') [-Wsign-conversion]
sumE += exp(vals[i] - m);
˜˜˜˜ ^
misc.cpp:76:21: warning: implicit conversion changes signedness: 'long' to 'size_type' (aka 'unsigned long') [-Wsign-conversion]
*ciLow = (*difs)[(long)(N/100.*cf)];
˜ ^˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜
misc.cpp:77:22: warning: implicit conversion changes signedness: 'long' to 'size_type' (aka 'unsigned long') [-Wsign-conversion]
*ciHigh = (*difs)[(long)(N-N/100.*cf)];
˜ ^˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜
5 warnings generated.
clang++ -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -DPACKAGE_NAME=\"Bitseq\" -DPACKAGE_TARNAME=\"bitseq\" -DPACKAGE_VERSION=\"1.4.x\" -DPACKAGE_STRING=\"Bitseq\ 1.4.x\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DBS_VERSION=\"1.4.2\" -DBIOC_BUILD=1 -D_USE_KNETFILE -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -I/usr/local/include -I"/Library/Frameworks/R.framework/Versions/3.0/Resources/library/Rsamtools/include" -I"/Library/Frameworks/R.framework/Versions/3.0/Resources/library/zlibbioc/include" -I. -fPIC -mtune=native -g -O2 -Wall -pedantic -Wconversion -c parseAlignment.cpp -o parseAlignment.o
In file included from parseAlignment.cpp:11:
./common.h:17:17: warning: variadic macros are a C99 feature [-Wvariadic-macros]
#define message(...) Rprintf(__VA_ARGS__)
^
In file included from parseAlignment.cpp:12:
./MyTimer.h:28:20: warning: implicit conversion changes signedness: 'long' to 'size_type' (aka 'unsigned long') [-Wsign-conversion]
times.resize(N);
˜˜˜˜˜ ^
./MyTimer.h:36:23: warning: implicit conversion changes signedness: 'long' to 'size_type' (aka 'unsigned long') [-Wsign-conversion]
times.resize(N);
˜˜˜˜˜ ^
./MyTimer.h:38:13: warning: implicit conversion changes signedness: 'long' to 'size_type' (aka 'unsigned long') [-Wsign-conversion]
times[timer]=time(NULL);
˜˜˜˜˜ ^˜˜˜˜
./MyTimer.h:43:28: warning: implicit conversion changes signedness: 'long' to 'size_type' (aka 'unsigned long') [-Wsign-conversion]
ret=time(NULL)-times[timer];
˜˜˜˜˜ ^˜˜˜˜
./MyTimer.h:46:13: warning: implicit conversion changes signedness: 'long' to 'size_type' (aka 'unsigned long') [-Wsign-conversion]
times[timer]=time(NULL);
˜˜˜˜˜ ^˜˜˜˜
./MyTimer.h:52:28: warning: implicit conversion changes signedness: 'long' to 'size_type' (aka 'unsigned long') [-Wsign-conversion]
ret=time(NULL)-times[timer];
˜˜˜˜˜ ^˜˜˜˜
./MyTimer.h:60:28: warning: implicit conversion changes signedness: 'long' to 'size_type' (aka 'unsigned long') [-Wsign-conversion]
ret=time(NULL)-times[timer];
˜˜˜˜˜ ^˜˜˜˜
./MyTimer.h:63:13: warning: implicit conversion changes signedness: 'long' to 'size_type' (aka 'unsigned long') [-Wsign-conversion]
times[timer]=time(NULL);
˜˜˜˜˜ ^˜˜˜˜
In file included from parseAlignment.cpp:13:
In file included from ./ReadDistribution.h:10:
./TranscriptSequence.h:55:27: warning: implicit conversion changes signedness: 'size_type' (aka 'unsigned long') to 'long' [-Wsign-conversion]
long getG(){ return geneNames.size(); }
˜˜˜˜˜˜ ^˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜
In file included from parseAlignment.cpp:13:
In file included from ./ReadDistribution.h:11:
./TranscriptExpression.h:32:38: warning: implicit conversion changes signedness: 'long' to 'size_type' (aka 'unsigned long') [-Wsign-conversion]
double exp(long tr){return trs[tr].exp;}
˜˜˜ ^˜
./TranscriptExpression.h:33:38: warning: implicit conversion changes signedness: 'long' to 'size_type' (aka 'unsigned long') [-Wsign-conversion]
double var(long tr){return trs[tr].var;}
˜˜˜ ^˜
./TranscriptExpression.h:34:35: warning: implicit conversion changes signedness: 'long' to 'size_type' (aka 'unsigned long') [-Wsign-conversion]
long id(long tr){return trs[tr].id;}
˜˜˜ ^˜
parseAlignment.cpp:311:38: warning: implicit conversion changes signedness: 'long' to 'size_type' (aka 'unsigned long') [-Wsign-conversion]
if(minProb>alignments[i].getLowProb())minProb = alignments[i].getLowProb();
˜˜˜˜˜˜˜˜˜˜ ^
parseAlignment.cpp:311:75: warning: implicit conversion changes signedness: 'long' to 'size_type' (aka 'unsigned long') [-Wsign-conversion]
if(minProb>alignments[i].getLowProb())minProb = alignments[i].getLowProb();
˜˜˜˜˜˜˜˜˜˜ ^
parseAlignment.cpp:312:38: warning: implicit conversion changes signedness: 'long' to 'size_type' (aka 'unsigned long') [-Wsign-conversion]
outF<<" "<<alignments[i].getTrId()
˜˜˜˜˜˜˜˜˜˜ ^
parseAlignment.cpp:314:38: warning: implicit conversion changes signedness: 'long' to 'size_type' (aka 'unsigned long') [-Wsign-conversion]
<<" "<<alignments[i].getProb();
˜˜˜˜˜˜˜˜˜˜ ^
parseAlignment.cpp:400:15: warning: implicit conversion changes signedness: 'long' to 'size_type' (aka 'unsigned long') [-Wsign-conversion]
if((str[i]>='A')&&(str[i]<='Z'))str[i]=str[i]-'A'+'a';
˜˜˜ ^
parseAlignment.cpp:400:30: warning: implicit conversion changes signedness: 'long' to 'size_type' (aka 'unsigned long') [-Wsign-conversion]
if((str[i]>='A')&&(str[i]<='Z'))str[i]=str[i]-'A'+'a';
˜˜˜ ^
parseAlignment.cpp:400:43: warning: implicit conversion changes signedness: 'long' to 'size_type' (aka 'unsigned long') [-Wsign-conversion]
if((str[i]>='A')&&(str[i]<='Z'))str[i]=str[i]-'A'+'a';
˜˜˜ ^
parseAlignment.cpp:400:50: warning: implicit conversion changes signedness: 'long' to 'size_type' (aka 'unsigned long') [-Wsign-conversion]
if((str[i]>='A')&&(str[i]<='Z'))str[i]=str[i]-'A'+'a';
˜˜˜ ^
parseAlignment.cpp:490:30: warning: implicit conversion changes signedness: 'long' to 'size_type' (aka 'unsigned long') [-Wsign-conversion]
vector<string> trNames(*M);
˜˜˜˜˜˜˜ ^˜
parseAlignment.cpp:491:30: warning: implicit conversion changes signedness: 'long' to 'size_type' (aka 'unsigned long') [-Wsign-conversion]
vector<long> trLengths(*M);
˜˜˜˜˜˜˜˜˜ ^˜
parseAlignment.cpp:493:18: warning: implicit conversion changes signedness: 'long' to 'size_type' (aka 'unsigned long') [-Wsign-conversion]
trNames[i] = samFile->header->target_name[i];
˜˜˜˜˜˜˜ ^
parseAlignment.cpp:494:20: warning: implicit conversion changes signedness: 'long' to 'size_type' (aka 'unsigned long') [-Wsign-conversion]
trLengths[i] = samFile->header->target_len[i];
˜˜˜˜˜˜˜˜˜ ^
parseAlignment.cpp:497:46: warning: implicit conversion changes signedness: 'long' to 'size_type' (aka 'unsigned long') [-Wsign-conversion]
if(! (*trInfo)->setInfo(vector<string>(*M,"none"), trNames, trLengths)){
˜˜˜˜˜˜ ^˜
26 warnings generated.
clang++ -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -DPACKAGE_NAME=\"Bitseq\" -DPACKAGE_TARNAME=\"bitseq\" -DPACKAGE_VERSION=\"1.4.x\" -DPACKAGE_STRING=\"Bitseq\ 1.4.x\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DBS_VERSION=\"1.4.2\" -DBIOC_BUILD=1 -D_USE_KNETFILE -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -I/usr/local/include -I"/Library/Frameworks/R.framework/Versions/3.0/Resources/library/Rsamtools/include" -I"/Library/Frameworks/R.framework/Versions/3.0/Resources/library/zlibbioc/include" -I. -fPIC -mtune=native -g -O2 -Wall -pedantic -Wconversion -c transposeFiles.cpp -o transposeFiles.o
In file included from transposeFiles.cpp:8:
./common.h:17:17: warning: variadic macros are a C99 feature [-Wvariadic-macros]
#define message(...) Rprintf(__VA_ARGS__)
^
transposeFiles.cpp:24:12: warning: implicit conversion changes signedness: 'size_type' (aka 'unsigned long') to 'long' [-Wsign-conversion]
fileN = inFileNames.size();
˜ ^˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜
transposeFiles.cpp:29:34: warning: implicit conversion changes signedness: 'long' to 'size_type' (aka 'unsigned long') [-Wsign-conversion]
inFile[i].open(inFileNames[i].c_str());
˜˜˜˜˜˜˜˜˜˜˜ ^
transposeFiles.cpp:32:82: warning: implicit conversion changes signedness: 'long' to 'size_type' (aka 'unsigned long') [-Wsign-conversion]
error("TransposeFile: Unable to read header of file: %s\n",(inFileNames[i]).c_str());
˜˜˜˜˜˜˜˜˜˜˜ ^
transposeFiles.cpp:40:111: warning: implicit conversion changes signedness: 'long' to 'size_type' (aka 'unsigned long') [-Wsign-conversion]
error("TransposeFile: Different number of transcripts or file %s is in wrong format.\n",(inFileNames[i]).c_str());
˜˜˜˜˜˜˜˜˜˜˜ ^
transposeFiles.cpp:43:34: warning: implicit conversion changes signedness: 'long' to 'size_type' (aka 'unsigned long') [-Wsign-conversion]
outFile<<"# "<<inFileNames[i]<<" "<<n<<endl;
˜˜˜˜˜˜˜˜˜˜˜ ^
transposeFiles.cpp:61:36: warning: implicit conversion changes signedness: 'long' to 'size_type' (aka 'unsigned long') [-Wsign-conversion]
vector< vector<long> > seeks(fileN,vector<long>(maxN,-1));
˜˜˜˜˜ ^˜˜˜˜
transposeFiles.cpp:61:55: warning: implicit conversion changes signedness: 'long' to 'size_type' (aka 'unsigned long') [-Wsign-conversion]
vector< vector<long> > seeks(fileN,vector<long>(maxN,-1));
˜˜˜˜˜˜ ^˜˜˜
transposeFiles.cpp:62:40: warning: implicit conversion changes signedness: 'long' to 'size_type' (aka 'unsigned long') [-Wsign-conversion]
vector<vector<string> > valueBuf(bufMax,vector<string>(totalN));
˜˜˜˜˜˜˜˜ ^˜˜˜˜˜
transposeFiles.cpp:62:62: warning: implicit conversion changes signedness: 'long' to 'size_type' (aka 'unsigned long') [-Wsign-conversion]
vector<vector<string> > valueBuf(bufMax,vector<string>(totalN));
˜˜˜˜˜˜ ^˜˜˜˜˜
transposeFiles.cpp:72:22: warning: implicit conversion changes signedness: 'long' to 'size_type' (aka 'unsigned long') [-Wsign-conversion]
for(i=0;i<N[f];i++){
˜ ^
transposeFiles.cpp:73:53: warning: implicit conversion changes signedness: 'long' to 'size_type' (aka 'unsigned long') [-Wsign-conversion]
for(j=0;j<bufN;j++) inFile[f]>>valueBuf[j][lastBuf];
˜˜˜˜˜˜˜˜ ^
transposeFiles.cpp:73:56: warning: implicit conversion changes signedness: 'long' to 'size_type' (aka 'unsigned long') [-Wsign-conversion]
for(j=0;j<bufN;j++) inFile[f]>>valueBuf[j][lastBuf];
˜˜˜˜˜˜˜˜ ^˜˜˜˜˜˜
transposeFiles.cpp:75:19: warning: implicit conversion changes signedness: 'long' to 'size_type' (aka 'unsigned long') [-Wsign-conversion]
seeks[f][i]=inFile[f].tellg();
˜˜˜˜˜ ^
transposeFiles.cpp:75:22: warning: implicit conversion changes signedness: 'long' to 'size_type' (aka 'unsigned long') [-Wsign-conversion]
seeks[f][i]=inFile[f].tellg();
˜˜˜˜˜ ^
transposeFiles.cpp:82:31: warning: implicit conversion changes signedness: 'long' to 'size_type' (aka 'unsigned long') [-Wsign-conversion]
outFile<<valueBuf[j][i]<<" ";
˜˜˜˜˜˜˜˜ ^
transposeFiles.cpp:82:34: warning: implicit conversion changes signedness: 'long' to 'size_type' (aka 'unsigned long') [-Wsign-conversion]
outFile<<valueBuf[j][i]<<" ";
˜˜˜˜˜˜˜˜ ^
transposeFiles.cpp:97:25: warning: implicit conversion changes signedness: 'long' to 'size_type' (aka 'unsigned long') [-Wsign-conversion]
for(i=0;i<N[f];i++){
˜ ^
transposeFiles.cpp:98:38: warning: implicit conversion changes signedness: 'long' to 'size_type' (aka 'unsigned long') [-Wsign-conversion]
inFile[f].seekg(seeks[f][i]);
˜˜˜˜˜ ^
transposeFiles.cpp:98:41: warning: implicit conversion changes signedness: 'long' to 'size_type' (aka 'unsigned long') [-Wsign-conversion]
inFile[f].seekg(seeks[f][i]);
˜˜˜˜˜ ^
transposeFiles.cpp:99:56: warning: implicit conversion changes signedness: 'long' to 'size_type' (aka 'unsigned long') [-Wsign-conversion]
for(j=0;j<bufN;j++) inFile[f]>>valueBuf[j][lastBuf];
˜˜˜˜˜˜˜˜ ^
transposeFiles.cpp:99:59: warning: implicit conversion changes signedness: 'long' to 'size_type' (aka 'unsigned long') [-Wsign-conversion]
for(j=0;j<bufN;j++) inFile[f]>>valueBuf[j][lastBuf];
˜˜˜˜˜˜˜˜ ^˜˜˜˜˜˜
transposeFiles.cpp:101:22: warning: implicit conversion changes signedness: 'long' to 'size_type' (aka 'unsigned long') [-Wsign-conversion]
seeks[f][i]=inFile[f].tellg();
˜˜˜˜˜ ^
transposeFiles.cpp:101:25: warning: implicit conversion changes signedness: 'long' to 'size_type' (aka 'unsigned long') [-Wsign-conversion]
seeks[f][i]=inFile[f].tellg();
˜˜˜˜˜ ^
transposeFiles.cpp:107:34: warning: implicit conversion changes signedness: 'long' to 'size_type' (aka 'unsigned long') [-Wsign-conversion]
outFile<<valueBuf[j][i]<<" ";
˜˜˜˜˜˜˜˜ ^
transposeFiles.cpp:107:37: warning: implicit conversion changes signedness: 'long' to 'size_type' (aka 'unsigned long') [-Wsign-conversion]
outFile<<valueBuf[j][i]<<" ";
˜˜˜˜˜˜˜˜ ^
transposeFiles.cpp:116:26: warning: implicit conversion changes signedness: 'long' to 'size_type' (aka 'unsigned long') [-Wsign-conversion]
vector<long> seeks(m,-1);
˜˜˜˜˜ ^
transposeFiles.cpp:117:40: warning: implicit conversion changes signedness: 'long' to 'size_type' (aka 'unsigned long') [-Wsign-conversion]
vector<vector<string> > valueBuf(m,vector<string>(bufMax));
˜˜˜˜˜˜˜˜ ^
transposeFiles.cpp:117:57: warning: implicit conversion changes signedness: 'long' to 'size_type' (aka 'unsigned long') [-Wsign-conversion]
vector<vector<string> > valueBuf(m,vector<string>(bufMax));
˜˜˜˜˜˜ ^˜˜˜˜˜
transposeFiles.cpp:120:23: warning: implicit conversion changes signedness: 'long' to 'size_type' (aka 'unsigned long') [-Wsign-conversion]
seeks.assign(M,-1);
˜˜˜˜˜ ^
transposeFiles.cpp:122:23: warning: implicit conversion changes signedness: 'long' to 'size_type' (aka 'unsigned long') [-Wsign-conversion]
while(done<N[f]){
˜ ^
transposeFiles.cpp:124:23: warning: implicit conversion changes signedness: 'long' to 'size_type' (aka 'unsigned long') [-Wsign-conversion]
if(bufN>N[f]-done)bufN=N[f]-done;
˜ ^
transposeFiles.cpp:124:38: warning: implicit conversion changes signedness: 'long' to 'size_type' (aka 'unsigned long') [-Wsign-conversion]
if(bufN>N[f]-done)bufN=N[f]-done;
˜ ^
transposeFiles.cpp:132:25: warning: implicit conversion changes signedness: 'long' to 'size_type' (aka 'unsigned long') [-Wsign-conversion]
if(seeks[j]!=-1)inFile[f].seekg(seeks[j]);
˜˜˜˜˜ ^
transposeFiles.cpp:132:54: warning: implicit conversion changes signedness: 'long' to 'size_type' (aka 'unsigned long') [-Wsign-conversion]
if(seeks[j]!=-1)inFile[f].seekg(seeks[j]);
˜˜˜˜˜ ^
transposeFiles.cpp:134:39: warning: implicit conversion changes signedness: 'long' to 'size_type' (aka 'unsigned long') [-Wsign-conversion]
inFile[f]>>valueBuf[j][i];
˜˜˜˜˜˜˜˜ ^
transposeFiles.cpp:134:42: warning: implicit conversion changes signedness: 'long' to 'size_type' (aka 'unsigned long') [-Wsign-conversion]
inFile[f]>>valueBuf[j][i];
˜˜˜˜˜˜˜˜ ^
transposeFiles.cpp:136:22: warning: implicit conversion changes signedness: 'long' to 'size_type' (aka 'unsigned long') [-Wsign-conversion]
seeks[j]=inFile[f].tellg();
˜˜˜˜˜ ^
transposeFiles.cpp:137:36: warning: implicit conversion changes signedness: 'long' to 'size_type' (aka 'unsigned long') [-Wsign-conversion]
if((j+1<M)&&(seeks[j+1]==-1))inFile[f].ignore(100000000,'\n');
˜˜˜˜˜ ˜^˜
transposeFiles.cpp:142:37: warning: implicit conversion changes signedness: 'long' to 'size_type' (aka 'unsigned long') [-Wsign-conversion]
outFile<<valueBuf[j][i]<<" ";
˜˜˜˜˜˜˜˜ ^
transposeFiles.cpp:142:40: warning: implicit conversion changes signedness: 'long' to 'size_type' (aka 'unsigned long') [-Wsign-conversion]
outFile<<valueBuf[j][i]<<" ";
˜˜˜˜˜˜˜˜ ^
41 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 BitSeq.so ArgumentParser.o CollapsedSampler.o FileHeader.o GibbsParameters.o GibbsSampler.o PosteriorSamples.o R_init_BitSeq.o ReadDistribution.o Sampler.o TagAlignments.o TranscriptExpression.o TranscriptInfo.o TranscriptSequence.o common.o estimateDE.o estimateExpression.o estimateHyperPar.o getGeneExpression.o getVariance.o getWithinGeneExpression.o lowess.o misc.o parseAlignment.o transposeFiles.o /Library/Frameworks/R.framework/Versions/3.0/Resources/library/Rsamtools/usrlib//libbam.a /Library/Frameworks/R.framework/Versions/3.0/Resources/library/Rsamtools/usrlib//libbcf.a /Library/Frameworks/R.framework/Versions/3.0/Resources/library/Rsamtools/usrlib//libtabix.a -lz -pthread -F/Library/Frameworks/R.framework/.. -framework R -Wl,-framework -Wl,CoreFoundation
clang: warning: argument unused during compilation: '-pthread'
installing to /Users/biocbuild/bbs-2.12-bioc/meat/BitSeq.buildbin-libdir/BitSeq/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 (BitSeq)
>>>>>>>
>>>>>>> FIXING LINKS FOR BitSeq.buildbin-libdir/BitSeq/libs//BitSeq.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" "BitSeq.buildbin-libdir/BitSeq/libs//BitSeq.so"
install_name_tool -change "/usr/local/lib/libgfortran.2.dylib" "/Library/Frameworks/R.framework/Versions/3.0/Resources/lib/libgfortran.2.dylib" "BitSeq.buildbin-libdir/BitSeq/libs//BitSeq.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" "BitSeq.buildbin-libdir/BitSeq/libs//BitSeq.so"
install_name_tool -change "/usr/local/lib/libreadline.dylib" "/Library/Frameworks/R.framework/Versions/3.0/Resources/lib/libreadline.dylib" "BitSeq.buildbin-libdir/BitSeq/libs//BitSeq.so"