xcms 1.36.0
Ralf Tautenhahn
| Snapshot Date: 2013-04-30 17:01:37 -0700 (Tue, 30 Apr 2013) | | URL: https://hedgehog.fhcrc.org/bioconductor/branches/RELEASE_2_12/madman/Rpacks/xcms | | Last Changed Rev: 75263 / Revision: 76155 | | Last Changed Date: 2013-04-03 14:32:27 -0700 (Wed, 03 Apr 2013) |
| george2 | Linux (Ubuntu 12.04.1 LTS) / x86_64 | OK | OK | |
| moscato2 | Windows Server 2008 R2 Enterprise SP1 (64-bit) / x64 | OK | OK | OK |
| petty | Mac OS X Snow Leopard (10.6.8) / x86_64 | OK | OK | OK |
| pelham | Mac OS X Snow Leopard (10.6.8) / x86_64 | OK | OK | [ OK ] |
>>>>>>>
>>>>>>> INSTALLATION WITH 'R CMD INSTALL --preclean --no-multiarch --library=xcms.buildbin-libdir xcms_1.36.0.tar.gz'
>>>>>>>
* installing *source* package 'xcms' ...
** libs
rm -f massifquant/xcms_massifquant.o massifquant/TrMgr.o massifquant/Tracker.o massifquant/SegProc.o massifquant/DataKeeper.o massifquant/OpOverload.o obiwarp/mat.o obiwarp/vec.o obiwarp/xcms_dynprog.o obiwarp/xcms_lmat.o xcms_obiwarp.o fastMatch.o mzClust_hclust.o mzROI.o util.o xcms.o
clang++ -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -I/usr/local/include -fPIC -mtune=native -g -O2 -Wall -pedantic -Wconversion -c massifquant/xcms_massifquant.cpp -o massifquant/xcms_massifquant.o
massifquant/xcms_massifquant.cpp:46:25: warning: implicit conversion changes signedness: 'uint32_t' (aka 'unsigned int') to 'int' [-Wsign-conversion]
int totalScanNums = dkeep.getTotalScanNumbers();
˜˜˜˜˜˜˜˜˜˜˜˜˜ ^˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜
massifquant/xcms_massifquant.cpp:122:6: warning: unused variable 'scanLength' [-Wunused-variable]
int scanLength = int(featInfo.at(5) - featInfo.at(4) + 1);
^
massifquant/xcms_massifquant.cpp:33:58: warning: unused variable 'vstcenter' [-Wunused-variable]
SEXP peaklist,entrylist,list_names,vmz,vmzmin,vmzmax,vstcenter,vscmin,vscmax,vintensity,vintenmax, vlength;
^
massifquant/xcms_massifquant.cpp:33:93: warning: unused variable 'vintenmax' [-Wunused-variable]
SEXP peaklist,entrylist,list_names,vmz,vmzmin,vmzmax,vstcenter,vscmin,vscmax,vintensity,vintenmax, vlength;
^
massifquant/xcms_massifquant.cpp:76:12: warning: unused variable 'maxScanNums' [-Wunused-variable]
double maxScanNums = double(scanrangeTo);
^
5 warnings generated.
clang++ -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -I/usr/local/include -fPIC -mtune=native -g -O2 -Wall -pedantic -Wconversion -c massifquant/TrMgr.cpp -o massifquant/TrMgr.o
massifquant/TrMgr.cpp:16:19: warning: implicit conversion turns floating-point number into integer: 'const double' to 'int' [-Wconversion]
currMissedMax(cmm),
˜^˜˜
massifquant/TrMgr.cpp:26:21: warning: implicit conversion changes signedness: 'int' to 'size_type' (aka 'unsigned long') [-Wsign-conversion]
delete trks[i];
˜˜˜˜ ^
massifquant/TrMgr.cpp:63:12: warning: implicit conversion loses integer precision: 'size_type' (aka 'unsigned long') to 'int' [-Wshorten-64-to-32]
return picIdx.size();
˜˜˜˜˜˜ ^˜˜˜˜˜˜˜˜˜˜˜˜
massifquant/TrMgr.cpp:67:12: warning: implicit conversion loses integer precision: 'size_type' (aka 'unsigned long') to 'int' [-Wshorten-64-to-32]
return actIdx.size();
˜˜˜˜˜˜ ^˜˜˜˜˜˜˜˜˜˜˜˜
massifquant/TrMgr.cpp:71:17: warning: implicit conversion changes signedness: 'int' to 'size_type' (aka 'unsigned long') [-Wsign-conversion]
return trks[i];
˜˜˜˜ ^
massifquant/TrMgr.cpp:84:21: warning: implicit conversion changes signedness: 'int' to 'size_type' (aka 'unsigned long') [-Wsign-conversion]
return trks[picIdx.at(i)]->getFeatureInfo(scanTime);
˜˜˜˜ ^˜˜˜˜˜˜˜˜˜˜˜
massifquant/TrMgr.cpp:84:31: warning: implicit conversion changes signedness: 'int' to 'size_type' (aka 'unsigned long') [-Wsign-conversion]
return trks[picIdx.at(i)]->getFeatureInfo(scanTime);
˜˜˜˜˜˜ ^
massifquant/TrMgr.cpp:100:10: warning: implicit conversion changes signedness: 'int' to 'size_type' (aka 'unsigned long') [-Wsign-conversion]
trks[actIdx.at(i)]->predictCentroid();
˜˜˜˜ ^˜˜˜˜˜˜˜˜˜˜˜
massifquant/TrMgr.cpp:101:20: warning: implicit conversion changes signedness: 'int' to 'size_type' (aka 'unsigned long') [-Wsign-conversion]
centIdx = trks[actIdx.at(i)]->claimDataIdx(mData,iData,predDist,minTrLen, scanBack);
˜˜˜˜ ^˜˜˜˜˜˜˜˜˜˜˜
massifquant/TrMgr.cpp:176:44: warning: implicit conversion changes signedness: 'int' to 'size_type' (aka 'unsigned long') [-Wsign-conversion]
restructFoundIdx.push_back(actIdx.at(collideIdx.at(0)));
˜˜˜˜˜˜ ^˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜
massifquant/TrMgr.cpp:191:42: warning: implicit conversion changes signedness: 'int' to 'size_type' (aka 'unsigned long') [-Wsign-conversion]
restructFoundIdx.push_back(actIdx.at(collideIdx.at(bestIdx)));
˜˜˜˜˜˜ ^˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜
massifquant/TrMgr.cpp:191:56: warning: implicit conversion changes signedness: 'int' to 'size_type' (aka 'unsigned long') [-Wsign-conversion]
restructFoundIdx.push_back(actIdx.at(collideIdx.at(bestIdx)));
˜˜˜˜˜˜˜˜˜˜ ^˜˜˜˜˜˜
massifquant/TrMgr.cpp:192:47: warning: implicit conversion changes signedness: 'int' to 'size_type' (aka 'unsigned long') [-Wsign-conversion]
moreMissIdx = collideIdx != collideIdx.at(bestIdx);
˜˜˜˜˜˜˜˜˜˜ ^˜˜˜˜˜˜
massifquant/TrMgr.cpp:197:40: warning: implicit conversion changes signedness: 'int' to 'size_type' (aka 'unsigned long') [-Wsign-conversion]
missActIdx.push_back(actIdx.at(collideIdx.at(*it_miss)));
˜˜˜˜˜˜ ^˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜
massifquant/TrMgr.cpp:197:54: warning: implicit conversion changes signedness: 'int' to 'size_type' (aka 'unsigned long') [-Wsign-conversion]
missActIdx.push_back(actIdx.at(collideIdx.at(*it_miss)));
˜˜˜˜˜˜˜˜˜˜ ^˜˜˜˜˜˜˜
massifquant/TrMgr.cpp:132:18: warning: implicit conversion loses integer precision: 'size_type' (aka 'unsigned long') to 'int' [-Wshorten-64-to-32]
int origLen = predDatIdx.size();
˜˜˜˜˜˜˜ ^˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜
massifquant/TrMgr.cpp:137:18: warning: implicit conversion loses integer precision: 'size_type' (aka 'unsigned long') to 'int' [-Wshorten-64-to-32]
int chgdLen = predDatIdx.size();
˜˜˜˜˜˜˜ ^˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜
massifquant/TrMgr.cpp:213:14: warning: implicit conversion changes signedness: 'int' to 'size_type' (aka 'unsigned long') [-Wsign-conversion]
trks[*it]->incrementMiss();
˜˜˜˜ ^˜˜
massifquant/TrMgr.cpp:216:18: warning: implicit conversion changes signedness: 'int' to 'size_type' (aka 'unsigned long') [-Wsign-conversion]
if (trks[*it]->getCurrMissed() > currMissedMax ||
˜˜˜˜ ^˜˜
massifquant/TrMgr.cpp:217:18: warning: implicit conversion changes signedness: 'int' to 'size_type' (aka 'unsigned long') [-Wsign-conversion]
trks[*it]->getCurrMissed() > trks[*it]->getTrLen() ||
˜˜˜˜ ^˜˜
massifquant/TrMgr.cpp:217:47: warning: implicit conversion changes signedness: 'int' to 'size_type' (aka 'unsigned long') [-Wsign-conversion]
trks[*it]->getCurrMissed() > trks[*it]->getTrLen() ||
˜˜˜˜ ^˜˜
massifquant/TrMgr.cpp:218:19: warning: implicit conversion changes signedness: 'int' to 'size_type' (aka 'unsigned long') [-Wsign-conversion]
(trks[*it]->getPredCounts()/2) > trks[*it]->getTrLen()) {
˜˜˜˜ ^˜˜
massifquant/TrMgr.cpp:218:51: warning: implicit conversion changes signedness: 'int' to 'size_type' (aka 'unsigned long') [-Wsign-conversion]
(trks[*it]->getPredCounts()/2) > trks[*it]->getTrLen()) {
˜˜˜˜ ^˜˜
massifquant/TrMgr.cpp:230:14: warning: implicit conversion changes signedness: 'const int' to 'size_type' (aka 'unsigned long') [-Wsign-conversion]
if (trks[i]->getTrLen() < minTrLen) {
˜˜˜˜ ^
massifquant/TrMgr.cpp:233:21: warning: implicit conversion changes signedness: 'const int' to 'size_type' (aka 'unsigned long') [-Wsign-conversion]
delete trks[i];
˜˜˜˜ ^
massifquant/TrMgr.cpp:234:14: warning: implicit conversion changes signedness: 'const int' to 'size_type' (aka 'unsigned long') [-Wsign-conversion]
trks[i] = NULL;
˜˜˜˜ ^
massifquant/TrMgr.cpp:238:36: warning: implicit conversion changes signedness: 'const int' to 'size_type' (aka 'unsigned long') [-Wsign-conversion]
std::list<double> iList = trks[i]->getIntensityList();
˜˜˜˜ ^
massifquant/TrMgr.cpp:243:21: warning: implicit conversion changes signedness: 'const int' to 'size_type' (aka 'unsigned long') [-Wsign-conversion]
delete trks[i];
˜˜˜˜ ^
massifquant/TrMgr.cpp:244:14: warning: implicit conversion changes signedness: 'const int' to 'size_type' (aka 'unsigned long') [-Wsign-conversion]
trks[i] = NULL;
˜˜˜˜ ^
massifquant/TrMgr.cpp:250:21: warning: implicit conversion changes signedness: 'const int' to 'size_type' (aka 'unsigned long') [-Wsign-conversion]
delete trks[i];
˜˜˜˜ ^
massifquant/TrMgr.cpp:251:14: warning: implicit conversion changes signedness: 'const int' to 'size_type' (aka 'unsigned long') [-Wsign-conversion]
trks[i] = NULL;
˜˜˜˜ ^
massifquant/TrMgr.cpp:266:28: warning: implicit conversion changes signedness: 'const int' to 'size_type' (aka 'unsigned long') [-Wsign-conversion]
bool change = trks[i]->performScanBack();
˜˜˜˜ ^
massifquant/TrMgr.cpp:268:18: warning: implicit conversion changes signedness: 'const int' to 'size_type' (aka 'unsigned long') [-Wsign-conversion]
trks[i]->computeMyXbar();
˜˜˜˜ ^
massifquant/TrMgr.cpp:289:14: warning: implicit conversion changes signedness: 'int' to 'size_type' (aka 'unsigned long') [-Wsign-conversion]
trks[*it_f]->makeZeroCurrMissed();
˜˜˜˜ ^˜˜˜˜
massifquant/TrMgr.cpp:290:14: warning: implicit conversion changes signedness: 'int' to 'size_type' (aka 'unsigned long') [-Wsign-conversion]
trks[*it_f]->incrementTrLen();
˜˜˜˜ ^˜˜˜˜
massifquant/TrMgr.cpp:291:14: warning: implicit conversion changes signedness: 'int' to 'size_type' (aka 'unsigned long') [-Wsign-conversion]
trks[*it_f]->innovateCentroid(mData.at(*it_d),
˜˜˜˜ ^˜˜˜˜
massifquant/TrMgr.cpp:291:48: warning: implicit conversion changes signedness: 'int' to 'size_type' (aka 'unsigned long') [-Wsign-conversion]
trks[*it_f]->innovateCentroid(mData.at(*it_d),
˜˜˜˜˜ ^˜˜˜˜
massifquant/TrMgr.cpp:292:46: warning: implicit conversion changes signedness: 'int' to 'size_type' (aka 'unsigned long') [-Wsign-conversion]
iData.at(*it_d),
˜˜˜˜˜ ^˜˜˜˜
massifquant/TrMgr.cpp:295:15: warning: implicit conversion changes signedness: 'int' to 'size_type' (aka 'unsigned long') [-Wsign-conversion]
mData[*it_d] = CLAIMEDPT;
˜˜˜˜˜ ^˜˜˜˜
massifquant/TrMgr.cpp:296:15: warning: implicit conversion changes signedness: 'int' to 'size_type' (aka 'unsigned long') [-Wsign-conversion]
iData[*it_d] = CLAIMEDPT;
˜˜˜˜˜ ^˜˜˜˜
massifquant/TrMgr.cpp:314:30: warning: implicit conversion changes signedness: 'unsigned int' to 'const int' [-Wsign-conversion]
currScanIdx, i,
^
massifquant/TrMgr.cpp:330:18: warning: implicit conversion changes signedness: 'int' to 'size_type' (aka 'unsigned long') [-Wsign-conversion]
if (trks[*it]->getTrLen() < 5) {
˜˜˜˜ ^˜˜
massifquant/TrMgr.cpp:335:40: warning: implicit conversion changes signedness: 'int' to 'size_type' (aka 'unsigned long') [-Wsign-conversion]
std::list<double> iList = trks[*it]->getIntensityList();
˜˜˜˜ ^˜˜
massifquant/TrMgr.cpp:355:32: warning: implicit conversion changes signedness: 'int' to 'size_type' (aka 'unsigned long') [-Wsign-conversion]
bool change = trks[*it]->performScanBack();
˜˜˜˜ ^˜˜
massifquant/TrMgr.cpp:357:22: warning: implicit conversion changes signedness: 'int' to 'size_type' (aka 'unsigned long') [-Wsign-conversion]
trks[*it]->computeMyXbar();
˜˜˜˜ ^˜˜
massifquant/TrMgr.cpp:370:14: warning: implicit conversion changes signedness: 'int' to 'size_type' (aka 'unsigned long') [-Wsign-conversion]
trks[*it_pic]->displayContents();
˜˜˜˜ ^˜˜˜˜˜˜
massifquant/TrMgr.cpp:392:14: warning: implicit conversion changes signedness: 'const int' to 'size_type' (aka 'unsigned long') [-Wsign-conversion]
if (d.at(*it) < tmpmin) {
˜ ^˜˜
massifquant/TrMgr.cpp:394:21: warning: implicit conversion changes signedness: 'const int' to 'size_type' (aka 'unsigned long') [-Wsign-conversion]
tmpmin = d.at(*it);
˜ ^˜˜
massifquant/TrMgr.cpp:414:29: warning: implicit conversion changes signedness: 'int' to 'size_type' (aka 'unsigned long') [-Wsign-conversion]
totalCents += trks[picIdx.at(i)]->getTrLen();
˜˜˜˜ ^˜˜˜˜˜˜˜˜˜˜˜
massifquant/TrMgr.cpp:417:41: warning: implicit conversion changes signedness: 'int' to 'size_type' (aka 'unsigned long') [-Wsign-conversion]
std::list<int> iscanList = trks[picIdx.at(i)]->getScanList();
˜˜˜˜ ^˜˜˜˜˜˜˜˜˜˜˜
massifquant/TrMgr.cpp:418:41: warning: implicit conversion changes signedness: 'int' to 'size_type' (aka 'unsigned long') [-Wsign-conversion]
std::list<int> icentList = trks[picIdx.at(i)]->getCentroidList();
˜˜˜˜ ^˜˜˜˜˜˜˜˜˜˜˜
massifquant/TrMgr.cpp:419:42: warning: implicit conversion changes signedness: 'int' to 'size_type' (aka 'unsigned long') [-Wsign-conversion]
std::list<double> imzList = trks[picIdx.at(i)]->getMzList();
˜˜˜˜ ^˜˜˜˜˜˜˜˜˜˜˜
massifquant/TrMgr.cpp:420:49: warning: implicit conversion changes signedness: 'int' to 'size_type' (aka 'unsigned long') [-Wsign-conversion]
std::list<double> iintensityList = trks[picIdx.at(i)]->getIntensityList();
˜˜˜˜ ^˜˜˜˜˜˜˜˜˜˜˜
massifquant/TrMgr.cpp:445:27: warning: implicit conversion changes signedness: 'int' to 'size_type' (aka 'unsigned long') [-Wsign-conversion]
int istart = trks[picIdx.at(i)]->getStartScanIdx();
˜˜˜˜ ^˜˜˜˜˜˜˜˜˜˜˜
massifquant/TrMgr.cpp:468:16: warning: implicit conversion changes signedness: 'int' to 'size_type' (aka 'unsigned long') [-Wsign-conversion]
picIdx[j] = it->second;
˜˜˜˜˜˜ ^
massifquant/TrMgr.cpp:486:25: warning: implicit conversion changes signedness: 'const int' to 'size_type' (aka 'unsigned long') [-Wsign-conversion]
delete trks[eIdx.at(i)];
˜˜˜˜ ^˜˜˜˜˜˜˜˜˜
massifquant/TrMgr.cpp:487:18: warning: implicit conversion changes signedness: 'const int' to 'size_type' (aka 'unsigned long') [-Wsign-conversion]
trks[eIdx.at(i)] = NULL;
˜˜˜˜ ^˜˜˜˜˜˜˜˜˜
massifquant/TrMgr.cpp:508:10: warning: implicit conversion changes signedness: 'int' to 'size_type' (aka 'unsigned long') [-Wsign-conversion]
trks[i]->computeMyXbar();
˜˜˜˜ ^
massifquant/TrMgr.cpp:509:10: warning: implicit conversion changes signedness: 'int' to 'size_type' (aka 'unsigned long') [-Wsign-conversion]
trks[i]->computeMyS2();
˜˜˜˜ ^
massifquant/TrMgr.cpp:510:29: warning: implicit conversion changes signedness: 'int' to 'size_type' (aka 'unsigned long') [-Wsign-conversion]
double mzTol = ppm*trks[i]->getXbar()/10e5;
˜˜˜˜ ^
massifquant/TrMgr.cpp:512:57: warning: implicit conversion changes signedness: 'int' to 'size_type' (aka 'unsigned long') [-Wsign-conversion]
double peakDeviance = fabs(computeAnyXbar(diff(trks[i]->getMzList())));
˜˜˜˜ ^
massifquant/TrMgr.cpp:522:37: warning: implicit conversion changes signedness: 'int' to 'size_type' (aka 'unsigned long') [-Wsign-conversion]
std::list<double> mzList = trks[i]->getMzList();
˜˜˜˜ ^
massifquant/TrMgr.cpp:526:29: warning: implicit conversion changes signedness: 'int' to 'unsigned long' [-Wsign-conversion]
int n = mzList.size() - midIdx;
˜ ^˜˜˜˜˜
massifquant/TrMgr.cpp:529:36: warning: implicit conversion changes signedness: 'int' to 'size_type' (aka 'unsigned long') [-Wsign-conversion]
std::vector<double> seizmo(n);
˜˜˜˜˜˜ ^
massifquant/TrMgr.cpp:531:25: warning: implicit conversion changes signedness: 'int' to 'size_t' (aka 'unsigned long') [-Wsign-conversion]
for (size_t j = midIdx; j < mzVec.size(); ++j) {
˜ ^˜˜˜˜˜
massifquant/TrMgr.cpp:532:20: warning: implicit conversion changes signedness: 'int' to 'size_type' (aka 'unsigned long') [-Wsign-conversion]
seizmo[k] = fabs(rmz.at(j) - mzVec.at(j));
˜˜˜˜˜˜ ^
massifquant/TrMgr.cpp:526:27: warning: implicit conversion loses integer precision: 'unsigned long' to 'int' [-Wshorten-64-to-32]
int n = mzList.size() - midIdx;
˜ ˜˜˜˜˜˜˜˜˜˜˜˜˜˜^˜˜˜˜˜˜˜
67 warnings generated.
clang++ -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -I/usr/local/include -fPIC -mtune=native -g -O2 -Wall -pedantic -Wconversion -c massifquant/Tracker.cpp -o massifquant/Tracker.o
massifquant/Tracker.cpp:171:13: warning: implicit conversion loses integer precision: 'size_type' (aka 'unsigned long') to 'int' [-Wshorten-64-to-32]
trLen = scanList.size();
˜ ^˜˜˜˜˜˜˜˜˜˜˜˜˜˜
In file included from massifquant/Tracker.cpp:8:
massifquant/Tracker.h:49:16: warning: private field 'r_val_i' is not used [-Wunused-private-field]
double r_val_i;
^
massifquant/Tracker.h:50:16: warning: private field 'p_val_i' is not used [-Wunused-private-field]
double p_val_i;
^
massifquant/Tracker.h:53:16: warning: private field 'r_val_m' is not used [-Wunused-private-field]
double r_val_m;
^
massifquant/Tracker.h:54:16: warning: private field 'p_val_m' is not used [-Wunused-private-field]
double p_val_m;
^
5 warnings generated.
clang++ -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -I/usr/local/include -fPIC -mtune=native -g -O2 -Wall -pedantic -Wconversion -c massifquant/SegProc.cpp -o massifquant/SegProc.o
massifquant/SegProc.cpp:18:37: warning: implicit conversion turns floating-point number into integer: 'double' to 'size_type' (aka 'unsigned long') [-Wconversion]
segClusters = std::vector<int> (origTrNum, 0);
˜˜˜ ^˜˜˜˜˜˜˜˜
massifquant/SegProc.cpp:34:15: warning: implicit conversion turns floating-point number into integer: 'double' to 'int' [-Wconversion]
int ppm = busybody.getPpm();
˜˜˜ ^˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜
massifquant/SegProc.cpp:61:51: warning: implicit conversion changes signedness: 'int' to 'size_type' (aka 'unsigned long') [-Wsign-conversion]
if (candIdx.size() == 0 || segClusters.at(i) != 0) { continue; }
˜˜˜˜˜˜˜˜˜˜˜ ^
massifquant/SegProc.cpp:62:21: warning: implicit conversion changes signedness: 'int' to 'size_type' (aka 'unsigned long') [-Wsign-conversion]
segClusters[i] = 1;
˜˜˜˜˜˜˜˜˜˜˜ ^
massifquant/SegProc.cpp:90:46: warning: implicit conversion loses integer precision: 'size_type' (aka 'unsigned long') to 'const int' [-Wshorten-64-to-32]
compareMeans(busybody, *it_i, edges, segIdx.size());
˜˜˜˜˜˜˜˜˜˜˜˜ ^˜˜˜˜˜˜˜˜˜˜˜˜
massifquant/SegProc.cpp:95:32: warning: implicit conversion loses integer precision: 'size_type' (aka 'unsigned long') to 'const value_type' (aka 'const int') [-Wshorten-64-to-32]
unionIdx.push_back(segIdx.size());
˜˜˜˜˜˜˜˜ ^˜˜˜˜˜˜˜˜˜˜˜˜
massifquant/SegProc.cpp:182:25: warning: implicit conversion changes signedness: 'int' to 'unsigned long' [-Wsign-conversion]
cleanSegIdx[segCounts + k] = iSegs2Union.at(k);
^˜˜˜˜˜˜˜˜ ˜
massifquant/SegProc.cpp:185:23: warning: implicit conversion changes signedness: 'int' to 'size_type' (aka 'unsigned long') [-Wsign-conversion]
cleanUnionIdx[cleanCounts] = segCounts;
˜˜˜˜˜˜˜˜˜˜˜˜˜ ^˜˜˜˜˜˜˜˜˜˜
massifquant/SegProc.cpp:146:27: warning: implicit conversion loses integer precision: 'size_type' (aka 'unsigned long') to 'int' [-Wshorten-64-to-32]
int jCounts = jSIdx.size();
˜˜˜˜˜˜˜ ^˜˜˜˜˜˜˜˜˜˜˜
massifquant/SegProc.cpp:148:26: warning: implicit conversion loses integer precision: 'const unsigned long' to 'int' [-Wshorten-64-to-32]
int maxSet = max(iSegs2Union.size(), jSIdx.size());
˜˜˜˜˜˜ ^˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜
massifquant/SegProc.cpp:281:26: warning: implicit conversion changes signedness: 'int' to 'size_type' (aka 'unsigned long') [-Wsign-conversion]
erasedPicIdx[j] = *it;
˜˜˜˜˜˜˜˜˜˜˜˜ ^
11 warnings generated.
clang++ -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -I/usr/local/include -fPIC -mtune=native -g -O2 -Wall -pedantic -Wconversion -c massifquant/DataKeeper.cpp -o massifquant/DataKeeper.o
massifquant/DataKeeper.cpp:22:14: warning: implicit conversion changes signedness: 'int' to 'uint32_t' (aka 'unsigned int') [-Wsign-conversion]
num_scans = lastScan;
˜ ^˜˜˜˜˜˜˜
massifquant/DataKeeper.cpp:45:33: warning: implicit conversion changes signedness: 'int' to 'size_type' (aka 'unsigned long') [-Wsign-conversion]
int start_pos = scan_idx.at(s);
˜˜˜˜˜˜˜˜ ^
massifquant/DataKeeper.cpp:46:34: warning: implicit conversion changes signedness: 'int' to 'size_type' (aka 'unsigned long') [-Wsign-conversion]
int stop_pos = scan_idx.at(s + 1);
˜˜˜˜˜˜˜˜ ˜˜^˜˜
massifquant/DataKeeper.cpp:52:18: warning: implicit conversion changes signedness: 'int' to 'size_type' (aka 'unsigned long') [-Wsign-conversion]
the_scan[copyvec_idx] = mz.at(i);
˜˜˜˜˜˜˜˜ ^˜˜˜˜˜˜˜˜˜˜
massifquant/DataKeeper.cpp:52:39: warning: implicit conversion changes signedness: 'int' to 'size_type' (aka 'unsigned long') [-Wsign-conversion]
the_scan[copyvec_idx] = mz.at(i);
˜˜ ^
massifquant/DataKeeper.cpp:65:33: warning: implicit conversion changes signedness: 'int' to 'size_type' (aka 'unsigned long') [-Wsign-conversion]
int start_pos = scan_idx.at(s);
˜˜˜˜˜˜˜˜ ^
massifquant/DataKeeper.cpp:66:34: warning: implicit conversion changes signedness: 'int' to 'size_type' (aka 'unsigned long') [-Wsign-conversion]
int stop_pos = scan_idx.at(s + 1);
˜˜˜˜˜˜˜˜ ˜˜^˜˜
massifquant/DataKeeper.cpp:73:16: warning: implicit conversion changes signedness: 'int' to 'size_type' (aka 'unsigned long') [-Wsign-conversion]
mzScan[copyvec_idx] = mz.at(i);
˜˜˜˜˜˜ ^˜˜˜˜˜˜˜˜˜˜
massifquant/DataKeeper.cpp:73:37: warning: implicit conversion changes signedness: 'int' to 'size_type' (aka 'unsigned long') [-Wsign-conversion]
mzScan[copyvec_idx] = mz.at(i);
˜˜ ^
massifquant/DataKeeper.cpp:74:19: warning: implicit conversion changes signedness: 'int' to 'size_type' (aka 'unsigned long') [-Wsign-conversion]
intenScan[copyvec_idx] = intensity.at(i);
˜˜˜˜˜˜˜˜˜ ^˜˜˜˜˜˜˜˜˜˜
massifquant/DataKeeper.cpp:74:47: warning: implicit conversion changes signedness: 'int' to 'size_type' (aka 'unsigned long') [-Wsign-conversion]
intenScan[copyvec_idx] = intensity.at(i);
˜˜˜˜˜˜˜˜˜ ^
massifquant/DataKeeper.cpp:99:38: warning: implicit conversion changes signedness: 'int' to 'size_type' (aka 'unsigned long') [-Wsign-conversion]
mzScan = std::vector<double>(N);
˜˜˜ ^
massifquant/DataKeeper.cpp:100:41: warning: implicit conversion changes signedness: 'int' to 'size_type' (aka 'unsigned long') [-Wsign-conversion]
intenScan = std::vector<double>(N);
˜˜˜ ^
massifquant/DataKeeper.cpp:104:20: warning: implicit conversion changes signedness: 'int' to 'size_type' (aka 'unsigned long') [-Wsign-conversion]
mzScan[i] = pmz[idx - 1];
˜˜˜˜˜˜ ^
massifquant/DataKeeper.cpp:105:23: warning: implicit conversion changes signedness: 'int' to 'size_type' (aka 'unsigned long') [-Wsign-conversion]
intenScan[i] = sqrt(pinten[idx - 1]);
˜˜˜˜˜˜˜˜˜ ^
massifquant/DataKeeper.cpp:118:33: warning: implicit conversion changes signedness: 'int' to 'size_type' (aka 'unsigned long') [-Wsign-conversion]
int start_pos = scan_idx.at(s);
˜˜˜˜˜˜˜˜ ^
massifquant/DataKeeper.cpp:119:34: warning: implicit conversion changes signedness: 'int' to 'size_type' (aka 'unsigned long') [-Wsign-conversion]
int stop_pos = scan_idx.at(s + 1);
˜˜˜˜˜˜˜˜ ˜˜^˜˜
massifquant/DataKeeper.cpp:124:18: warning: implicit conversion changes signedness: 'int' to 'size_type' (aka 'unsigned long') [-Wsign-conversion]
the_scan[copyvec_idx] = intensity.at(i);
˜˜˜˜˜˜˜˜ ^˜˜˜˜˜˜˜˜˜˜
massifquant/DataKeeper.cpp:124:46: warning: implicit conversion changes signedness: 'int' to 'size_type' (aka 'unsigned long') [-Wsign-conversion]
the_scan[copyvec_idx] = intensity.at(i);
˜˜˜˜˜˜˜˜˜ ^
massifquant/DataKeeper.cpp:132:33: warning: implicit conversion changes signedness: 'int' to 'size_type' (aka 'unsigned long') [-Wsign-conversion]
int start_pos = scan_idx.at(s);
˜˜˜˜˜˜˜˜ ^
massifquant/DataKeeper.cpp:133:34: warning: implicit conversion changes signedness: 'int' to 'size_type' (aka 'unsigned long') [-Wsign-conversion]
int stop_pos = scan_idx.at(s + 1);
˜˜˜˜˜˜˜˜ ˜˜^˜˜
massifquant/DataKeeper.cpp:139:18: warning: implicit conversion changes signedness: 'int' to 'size_type' (aka 'unsigned long') [-Wsign-conversion]
the_scan[copyvec_idx] = mz.at(i);
˜˜˜˜˜˜˜˜ ^˜˜˜˜˜˜˜˜˜˜
massifquant/DataKeeper.cpp:139:39: warning: implicit conversion changes signedness: 'int' to 'size_type' (aka 'unsigned long') [-Wsign-conversion]
the_scan[copyvec_idx] = mz.at(i);
˜˜ ^
massifquant/DataKeeper.cpp:147:33: warning: implicit conversion changes signedness: 'int' to 'size_type' (aka 'unsigned long') [-Wsign-conversion]
int start_pos = scan_idx.at(s);
˜˜˜˜˜˜˜˜ ^
massifquant/DataKeeper.cpp:148:34: warning: implicit conversion changes signedness: 'int' to 'size_type' (aka 'unsigned long') [-Wsign-conversion]
int stop_pos = scan_idx.at(s + 1);
˜˜˜˜˜˜˜˜ ˜˜^˜˜
massifquant/DataKeeper.cpp:153:18: warning: implicit conversion changes signedness: 'int' to 'size_type' (aka 'unsigned long') [-Wsign-conversion]
the_scan[copyvec_idx] = intensity.at(i);
˜˜˜˜˜˜˜˜ ^˜˜˜˜˜˜˜˜˜˜
massifquant/DataKeeper.cpp:153:46: warning: implicit conversion changes signedness: 'int' to 'size_type' (aka 'unsigned long') [-Wsign-conversion]
the_scan[copyvec_idx] = intensity.at(i);
˜˜˜˜˜˜˜˜˜ ^
massifquant/DataKeeper.cpp:180:38: warning: implicit conversion changes signedness: 'int' to 'size_type' (aka 'unsigned long') [-Wsign-conversion]
mzScan = std::vector<double>(N);
˜˜˜ ^
massifquant/DataKeeper.cpp:181:41: warning: implicit conversion changes signedness: 'int' to 'size_type' (aka 'unsigned long') [-Wsign-conversion]
intenScan = std::vector<double>(N);
˜˜˜ ^
massifquant/DataKeeper.cpp:186:20: warning: implicit conversion changes signedness: 'int' to 'size_type' (aka 'unsigned long') [-Wsign-conversion]
mzScan[i] = pmz[idx - 1];
˜˜˜˜˜˜ ^
massifquant/DataKeeper.cpp:187:23: warning: implicit conversion changes signedness: 'int' to 'size_type' (aka 'unsigned long') [-Wsign-conversion]
intenScan[i] = pinten[idx - 1];
˜˜˜˜˜˜˜˜˜ ^
massifquant/DataKeeper.cpp:295:42: warning: implicit conversion changes signedness: 'int' to 'size_type' (aka 'unsigned long') [-Wsign-conversion]
mMaxFeat.push_back(mGhost.at(neighborIdx.at(imaxIdx)));
˜˜˜˜˜˜ ^˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜
massifquant/DataKeeper.cpp:295:57: warning: implicit conversion changes signedness: 'int' to 'size_type' (aka 'unsigned long') [-Wsign-conversion]
mMaxFeat.push_back(mGhost.at(neighborIdx.at(imaxIdx)));
˜˜˜˜˜˜˜˜˜˜˜ ^˜˜˜˜˜˜
massifquant/DataKeeper.cpp:321:27: warning: implicit conversion changes signedness: 'int' to 'size_type' (aka 'unsigned long') [-Wsign-conversion]
double mzApex = mz.at(apexIdx);
˜˜ ^˜˜˜˜˜˜
massifquant/DataKeeper.cpp:395:42: warning: implicit conversion changes signedness: 'int' to 'size_type' (aka 'unsigned long') [-Wsign-conversion]
mMaxFeat.push_back(mGhost.at(neighborIdx.at(imaxIdx)));
˜˜˜˜˜˜ ^˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜
massifquant/DataKeeper.cpp:395:57: warning: implicit conversion changes signedness: 'int' to 'size_type' (aka 'unsigned long') [-Wsign-conversion]
mMaxFeat.push_back(mGhost.at(neighborIdx.at(imaxIdx)));
˜˜˜˜˜˜˜˜˜˜˜ ^˜˜˜˜˜˜
In file included from massifquant/DataKeeper.cpp:4:
massifquant/DataKeeper.h:36:26: warning: private field 'scbuf' is not used [-Wunused-private-field]
struct scanBuf * scbuf;
^
37 warnings generated.
clang++ -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -I/usr/local/include -fPIC -mtune=native -g -O2 -Wall -pedantic -Wconversion -c massifquant/OpOverload.cpp -o massifquant/OpOverload.o
massifquant/OpOverload.cpp:32:7: warning: implicit conversion changes signedness: 'int' to 'size_type' (aka 'unsigned long') [-Wsign-conversion]
C[j] = A[j] + B[j];
˜ ^
massifquant/OpOverload.cpp:32:14: warning: implicit conversion changes signedness: 'int' to 'size_type' (aka 'unsigned long') [-Wsign-conversion]
C[j] = A[j] + B[j];
˜ ^
massifquant/OpOverload.cpp:32:21: warning: implicit conversion changes signedness: 'int' to 'size_type' (aka 'unsigned long') [-Wsign-conversion]
C[j] = A[j] + B[j];
˜ ^
massifquant/OpOverload.cpp:29:11: warning: implicit conversion loses integer precision: 'size_type' (aka 'unsigned long') to 'int' [-Wshorten-64-to-32]
int m = A.size();
˜ ^˜˜˜˜˜˜˜
massifquant/OpOverload.cpp:42:11: warning: implicit conversion changes signedness: 'int' to 'size_type' (aka 'unsigned long') [-Wsign-conversion]
C[j] = A[j] + B[j];
˜ ^
massifquant/OpOverload.cpp:42:18: warning: implicit conversion changes signedness: 'int' to 'size_type' (aka 'unsigned long') [-Wsign-conversion]
C[j] = A[j] + B[j];
˜ ^
massifquant/OpOverload.cpp:42:25: warning: implicit conversion changes signedness: 'int' to 'size_type' (aka 'unsigned long') [-Wsign-conversion]
C[j] = A[j] + B[j];
˜ ^
massifquant/OpOverload.cpp:39:11: warning: implicit conversion loses integer precision: 'size_type' (aka 'unsigned long') to 'int' [-Wshorten-64-to-32]
int m = A.size();
˜ ^˜˜˜˜˜˜˜
massifquant/OpOverload.cpp:52:7: warning: implicit conversion changes signedness: 'int' to 'size_type' (aka 'unsigned long') [-Wsign-conversion]
C[j] = A[j] - b;
˜ ^
massifquant/OpOverload.cpp:52:14: warning: implicit conversion changes signedness: 'int' to 'size_type' (aka 'unsigned long') [-Wsign-conversion]
C[j] = A[j] - b;
˜ ^
massifquant/OpOverload.cpp:49:11: warning: implicit conversion loses integer precision: 'size_type' (aka 'unsigned long') to 'int' [-Wshorten-64-to-32]
int m = A.size();
˜ ^˜˜˜˜˜˜˜
massifquant/OpOverload.cpp:63:7: warning: implicit conversion changes signedness: 'int' to 'size_type' (aka 'unsigned long') [-Wsign-conversion]
C[j] = A[j] / b;
˜ ^
massifquant/OpOverload.cpp:63:14: warning: implicit conversion changes signedness: 'int' to 'size_type' (aka 'unsigned long') [-Wsign-conversion]
C[j] = A[j] / b;
˜ ^
massifquant/OpOverload.cpp:60:11: warning: implicit conversion loses integer precision: 'size_type' (aka 'unsigned long') to 'int' [-Wshorten-64-to-32]
int m = A.size();
˜ ^˜˜˜˜˜˜˜
massifquant/OpOverload.cpp:75:14: warning: implicit conversion changes signedness: 'int' to 'size_type' (aka 'unsigned long') [-Wsign-conversion]
if (A.at(i) >= b)
˜ ^
massifquant/OpOverload.cpp:76:12: warning: implicit conversion changes signedness: 'int' to 'size_type' (aka 'unsigned long') [-Wsign-conversion]
C.at(i) = 1;
˜ ^
massifquant/OpOverload.cpp:72:11: warning: implicit conversion loses integer precision: 'size_type' (aka 'unsigned long') to 'int' [-Wshorten-64-to-32]
int m = A.size();
˜ ^˜˜˜˜˜˜˜
massifquant/OpOverload.cpp:86:14: warning: implicit conversion changes signedness: 'int' to 'size_type' (aka 'unsigned long') [-Wsign-conversion]
if (A.at(i) <= b)
˜ ^
massifquant/OpOverload.cpp:87:12: warning: implicit conversion changes signedness: 'int' to 'size_type' (aka 'unsigned long') [-Wsign-conversion]
C.at(i) = 1;
˜ ^
massifquant/OpOverload.cpp:83:11: warning: implicit conversion loses integer precision: 'size_type' (aka 'unsigned long') to 'int' [-Wshorten-64-to-32]
int m = A.size();
˜ ^˜˜˜˜˜˜˜
massifquant/OpOverload.cpp:97:14: warning: implicit conversion changes signedness: 'int' to 'size_type' (aka 'unsigned long') [-Wsign-conversion]
if (A.at(i) == b)
˜ ^
massifquant/OpOverload.cpp:94:11: warning: implicit conversion loses integer precision: 'size_type' (aka 'unsigned long') to 'int' [-Wshorten-64-to-32]
int m = A.size();
˜ ^˜˜˜˜˜˜˜
massifquant/OpOverload.cpp:168:14: warning: implicit conversion changes signedness: 'int' to 'size_type' (aka 'unsigned long') [-Wsign-conversion]
if (A.at(i) > b)
˜ ^
massifquant/OpOverload.cpp:169:12: warning: implicit conversion changes signedness: 'int' to 'size_type' (aka 'unsigned long') [-Wsign-conversion]
C.at(i) = 1;
˜ ^
massifquant/OpOverload.cpp:165:11: warning: implicit conversion loses integer precision: 'size_type' (aka 'unsigned long') to 'int' [-Wshorten-64-to-32]
int m = A.size();
˜ ^˜˜˜˜˜˜˜
massifquant/OpOverload.cpp:179:14: warning: implicit conversion changes signedness: 'int' to 'size_type' (aka 'unsigned long') [-Wsign-conversion]
if (A.at(i) >= b)
˜ ^
massifquant/OpOverload.cpp:180:12: warning: implicit conversion changes signedness: 'int' to 'size_type' (aka 'unsigned long') [-Wsign-conversion]
C.at(i) = 1;
˜ ^
massifquant/OpOverload.cpp:176:11: warning: implicit conversion loses integer precision: 'size_type' (aka 'unsigned long') to 'int' [-Wshorten-64-to-32]
int m = A.size();
˜ ^˜˜˜˜˜˜˜
massifquant/OpOverload.cpp:190:14: warning: implicit conversion changes signedness: 'int' to 'size_type' (aka 'unsigned long') [-Wsign-conversion]
if (A.at(i) <= b)
˜ ^
massifquant/OpOverload.cpp:191:12: warning: implicit conversion changes signedness: 'int' to 'size_type' (aka 'unsigned long') [-Wsign-conversion]
C.at(i) = 1;
˜ ^
massifquant/OpOverload.cpp:187:11: warning: implicit conversion loses integer precision: 'size_type' (aka 'unsigned long') to 'int' [-Wshorten-64-to-32]
int m = A.size();
˜ ^˜˜˜˜˜˜˜
massifquant/OpOverload.cpp:211:7: warning: implicit conversion changes signedness: 'int' to 'size_type' (aka 'unsigned long') [-Wsign-conversion]
C[j] = A[j]*B[j];
˜ ^
massifquant/OpOverload.cpp:211:14: warning: implicit conversion changes signedness: 'int' to 'size_type' (aka 'unsigned long') [-Wsign-conversion]
C[j] = A[j]*B[j];
˜ ^
massifquant/OpOverload.cpp:211:19: warning: implicit conversion changes signedness: 'int' to 'size_type' (aka 'unsigned long') [-Wsign-conversion]
C[j] = A[j]*B[j];
˜ ^
massifquant/OpOverload.cpp:208:11: warning: implicit conversion loses integer precision: 'size_type' (aka 'unsigned long') to 'int' [-Wshorten-64-to-32]
int m = A.size();
˜ ^˜˜˜˜˜˜˜
massifquant/OpOverload.cpp:221:7: warning: implicit conversion changes signedness: 'int' to 'size_type' (aka 'unsigned long') [-Wsign-conversion]
C[j] = A[j] + B[j];
˜ ^
massifquant/OpOverload.cpp:221:14: warning: implicit conversion changes signedness: 'int' to 'size_type' (aka 'unsigned long') [-Wsign-conversion]
C[j] = A[j] + B[j];
˜ ^
massifquant/OpOverload.cpp:221:21: warning: implicit conversion changes signedness: 'int' to 'size_type' (aka 'unsigned long') [-Wsign-conversion]
C[j] = A[j] + B[j];
˜ ^
massifquant/OpOverload.cpp:218:11: warning: implicit conversion loses integer precision: 'size_type' (aka 'unsigned long') to 'int' [-Wshorten-64-to-32]
int m = A.size();
˜ ^˜˜˜˜˜˜˜
massifquant/OpOverload.cpp:233:17: warning: implicit conversion changes signedness: 'int' to 'size_type' (aka 'unsigned long') [-Wsign-conversion]
Asubset[i] = A.at(*it); //assign it the current value;
˜˜˜˜˜˜˜ ^
massifquant/OpOverload.cpp:233:27: warning: implicit conversion changes signedness: 'const int' to 'size_type' (aka 'unsigned long') [-Wsign-conversion]
Asubset[i] = A.at(*it); //assign it the current value;
˜ ^˜˜
massifquant/OpOverload.cpp:228:11: warning: implicit conversion loses integer precision: 'size_type' (aka 'unsigned long') to 'int' [-Wshorten-64-to-32]
int m = subidx.size();
˜ ^˜˜˜˜˜˜˜˜˜˜˜˜
massifquant/OpOverload.cpp:246:17: warning: implicit conversion changes signedness: 'int' to 'size_type' (aka 'unsigned long') [-Wsign-conversion]
Asubset[i] = A.at(*it); //assign it the current value;
˜˜˜˜˜˜˜ ^
massifquant/OpOverload.cpp:246:27: warning: implicit conversion changes signedness: 'const int' to 'size_type' (aka 'unsigned long') [-Wsign-conversion]
Asubset[i] = A.at(*it); //assign it the current value;
˜ ^˜˜
massifquant/OpOverload.cpp:241:13: warning: implicit conversion loses integer precision: 'size_type' (aka 'unsigned long') to 'int' [-Wshorten-64-to-32]
int m = subidx.size();
˜ ^˜˜˜˜˜˜˜˜˜˜˜˜
massifquant/OpOverload.cpp:260:13: warning: implicit conversion changes signedness: 'int' to 'size_type' (aka 'unsigned long') [-Wsign-conversion]
seq[count] = i;
˜˜˜ ^˜˜˜˜
massifquant/OpOverload.cpp:328:24: warning: implicit conversion changes signedness: 'int' to 'size_type' (aka 'unsigned long') [-Wsign-conversion]
if ( mzvals.at(mid) < val){
˜˜˜˜˜˜ ^˜˜
massifquant/OpOverload.cpp:344:29: warning: implicit conversion changes signedness: 'int' to 'size_type' (aka 'unsigned long') [-Wsign-conversion]
if (val < mzvals.at(mid) ){
˜˜˜˜˜˜ ^˜˜
48 warnings generated.
clang++ -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -I/usr/local/include -fPIC -mtune=native -g -O2 -Wall -pedantic -Wconversion -c obiwarp/mat.cpp -o obiwarp/mat.o
obiwarp/mat.cpp:416:45: warning: implicit conversion changes signedness: 'int' to 'size_t' (aka 'unsigned long') [-Wsign-conversion]
fwrite((int*)(_dat), sizeof(int), _m*_n, fh);
˜˜˜˜˜˜ ˜˜^˜˜
obiwarp/mat.cpp:824:51: warning: implicit conversion changes signedness: 'int' to 'size_t' (aka 'unsigned long') [-Wsign-conversion]
fwrite((double*)(_dat), sizeof(double), _m*_n, fh);
˜˜˜˜˜˜ ˜˜^˜˜
obiwarp/mat.cpp:1242:49: warning: implicit conversion changes signedness: 'int' to 'size_t' (aka 'unsigned long') [-Wsign-conversion]
fwrite((float*)(_dat), sizeof(float), _m*_n, fh);
˜˜˜˜˜˜ ˜˜^˜˜
3 warnings generated.
clang++ -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -I/usr/local/include -fPIC -mtune=native -g -O2 -Wall -pedantic -Wconversion -c obiwarp/vec.cpp -o obiwarp/vec.o
obiwarp/vec.cpp:406:17: warning: implicit conversion changes signedness: 'int' to 'size_t' (aka 'unsigned long') [-Wsign-conversion]
qsort(_dat, _n, sizeof(int), intCompare);
˜˜˜˜˜ ^˜
obiwarp/vec.cpp:1423:17: warning: implicit conversion changes signedness: 'int' to 'size_t' (aka 'unsigned long') [-Wsign-conversion]
qsort(_dat, _n, sizeof(double), doubleCompare);
˜˜˜˜˜ ^˜
obiwarp/vec.cpp:2440:17: warning: implicit conversion changes signedness: 'int' to 'size_t' (aka 'unsigned long') [-Wsign-conversion]
qsort(_dat, _n, sizeof(float), floatCompare);
˜˜˜˜˜ ^˜
3 warnings generated.
clang++ -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -I/usr/local/include -fPIC -mtune=native -g -O2 -Wall -pedantic -Wconversion -c obiwarp/xcms_dynprog.cpp -o obiwarp/xcms_dynprog.o
In file included from obiwarp/xcms_dynprog.cpp:6:
obiwarp/xcms_dynprog.h:69:23: warning: implicit conversion loses floating-point precision: 'double' to 'float' [-Wconversion]
val = pow(i,order);
˜ ^˜˜˜˜˜˜˜˜˜˜˜
obiwarp/xcms_dynprog.cpp:482:21: warning: implicit conversion loses floating-point precision: 'double' to 'float' [-Wconversion]
sum_sq_res_yeqx = VecF::sum_sq_res_yeqx(nVals, nValsNew);
˜ ^˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜
obiwarp/xcms_dynprog.cpp:534:10: warning: implicit conversion loses floating-point precision: 'double' to 'float' [-Wconversion]
return VecF::sum_sq_res_yeqx(nVals, nValsNew);
˜˜˜˜˜˜ ^˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜
obiwarp/xcms_dynprog.cpp:582:34: warning: implicit conversion loses floating-point precision: 'double' to 'float' [-Wconversion]
((sum_x[n] * sum_y[m])/cols))/cols;
˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜^˜˜˜˜
obiwarp/xcms_dynprog.cpp:724:18: warning: implicit conversion loses floating-point precision: 'double' to 'float' [-Wconversion]
tmp(m,n) = sqrt(sum);
˜ ^˜˜˜˜˜˜˜˜
obiwarp/xcms_dynprog.cpp:921:16: warning: implicit conversion loses floating-point precision: 'double' to 'float' [-Wconversion]
float _avg = smat.avg();
˜˜˜˜ ^˜˜˜˜˜˜˜˜˜
6 warnings generated.
clang++ -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -I/usr/local/include -fPIC -mtune=native -g -O2 -Wall -pedantic -Wconversion -c obiwarp/xcms_lmat.cpp -o obiwarp/xcms_lmat.o
obiwarp/xcms_lmat.cpp:41:19: warning: implicit conversion loses floating-point precision: 'double' to 'float' [-Wconversion]
tm_tmp[i] = pscantime[i];
˜ ^˜˜˜˜˜˜˜˜˜˜˜
obiwarp/xcms_lmat.cpp:50:19: warning: implicit conversion loses floating-point precision: 'double' to 'float' [-Wconversion]
mz_tmp[i] = mz[i];
˜ ^˜˜˜˜
obiwarp/xcms_lmat.cpp:59:20: warning: implicit conversion loses floating-point precision: 'double' to 'float' [-Wconversion]
mat_tmp[i] = intensity[i];
˜ ^˜˜˜˜˜˜˜˜˜˜˜
obiwarp/xcms_lmat.cpp:129:17: warning: implicit conversion loses integer precision: 'size_t' (aka 'unsigned long') to 'int' [-Wshorten-64-to-32]
int len = strlen( str );
˜˜˜ ^˜˜˜˜˜˜˜˜˜˜˜˜
4 warnings generated.
clang++ -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -I/usr/local/include -fPIC -mtune=native -g -O2 -Wall -pedantic -Wconversion -c xcms_obiwarp.cpp -o xcms_obiwarp.o
In file included from xcms_obiwarp.cpp:12:
./obiwarp/xcms_dynprog.h:69:23: warning: implicit conversion loses floating-point precision: 'double' to 'float' [-Wconversion]
val = pow(i,order);
˜ ^˜˜˜˜˜˜˜˜˜˜˜
xcms_obiwarp.cpp:101:28: warning: implicit conversion loses floating-point precision: 'double' to 'float' [-Wconversion]
dyn.linear_less_before(*REAL(gap_extend), *REAL(gap_init), gp_length, gp_array);
˜˜˜ ^˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜
xcms_obiwarp.cpp:101:47: warning: implicit conversion loses floating-point precision: 'double' to 'float' [-Wconversion]
dyn.linear_less_before(*REAL(gap_extend), *REAL(gap_init), gp_length, gp_array);
˜˜˜ ^˜˜˜˜˜˜˜˜˜˜˜˜˜˜
xcms_obiwarp.cpp:111:5: warning: implicit conversion loses floating-point precision: 'double' to 'float' [-Wconversion]
*REAL(factor_diag), *REAL(factor_gap), *INTEGER(AS_INTEGER(local_alignment)), *REAL(init_penalty));
^˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜
xcms_obiwarp.cpp:111:25: warning: implicit conversion loses floating-point precision: 'double' to 'float' [-Wconversion]
*REAL(factor_diag), *REAL(factor_gap), *INTEGER(AS_INTEGER(local_alignment)), *REAL(init_penalty));
^˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜
xcms_obiwarp.cpp:111:83: warning: implicit conversion loses floating-point precision: 'double' to 'float' [-Wconversion]
*REAL(factor_diag), *REAL(factor_gap), *INTEGER(AS_INTEGER(local_alignment)), *REAL(init_penalty));
^˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜
6 warnings generated.
clang -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -I/usr/local/include -fPIC -mtune=native -g -O2 -Wall -pedantic -Wconversion -c fastMatch.c -o fastMatch.o
fastMatch.c:30:61: warning: implicit conversion changes signedness: 'int' to 'size_t' (aka 'unsigned long') [-Wsign-conversion]
struct idxStruct * pidxS = (struct idxStruct *) calloc(nx, sizeof(struct idxStruct));
˜˜˜˜˜˜ ^˜
fastMatch.c:32:81: warning: implicit conversion changes signedness: 'int' to 'unsigned long' [-Wsign-conversion]
error("fastMatch/calloc: memory could not be allocated ! (%d bytes)\n", nx * sizeof(struct idxStruct) );
^˜ ˜
2 warnings generated.
clang -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -I/usr/local/include -fPIC -mtune=native -g -O2 -Wall -pedantic -Wconversion -c mzClust_hclust.c -o mzClust_hclust.o
mzClust_hclust.c:29:27: warning: implicit conversion changes signedness: 'int' to 'unsigned long' [-Wsign-conversion]
clust = (int *) malloc(n * m * sizeof(int));
˜˜^˜˜ ˜
1 warning generated.
clang -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -I/usr/local/include -fPIC -mtune=native -g -O2 -Wall -pedantic -Wconversion -c mzROI.c -o mzROI.o
mzROI.c:68:37: warning: implicit conversion turns floating-point number into integer: 'double' to 'unsigned int' [-Wconversion]
newLength= mzLength->mzROITotal * ROI_ALLOC_INC;
˜ ˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜^˜˜˜˜˜˜˜˜˜˜˜˜˜˜
mzROI.c:91:38: warning: implicit conversion turns floating-point number into integer: 'double' to 'unsigned int' [-Wconversion]
newLength= mzLength->mzvalTotal * MZVAL_ALLOC_INC;
˜ ˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜^˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜
mzROI.c:181:58: warning: implicit conversion changes signedness: 'unsigned int' to 'int' [-Wsign-conversion]
int lpos = lower_bound( fMass - ddev,mzval,0,mzLength->mzval);
˜˜˜˜˜˜˜˜˜˜˜ ˜˜˜˜˜˜˜˜˜˜^˜˜˜˜
mzROI.c:182:67: warning: implicit conversion changes signedness: 'unsigned int' to 'int' [-Wsign-conversion]
int hpos = upper_bound( fMass + ddev,mzval,lpos,mzLength->mzval - lpos);
˜˜˜˜˜˜˜˜˜˜˜ ˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜^˜˜˜˜˜
mzROI.c:182:69: warning: implicit conversion changes signedness: 'int' to 'unsigned int' [-Wsign-conversion]
int hpos = upper_bound( fMass + ddev,mzval,lpos,mzLength->mzval - lpos);
˜ ^˜˜˜
mzROI.c:185:30: warning: implicit conversion changes signedness: 'unsigned int' to 'int' [-Wsign-conversion]
lpos = mzLength->mzval -1;
˜ ˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜^˜
mzROI.c:187:30: warning: implicit conversion changes signedness: 'unsigned int' to 'int' [-Wsign-conversion]
hpos = mzLength->mzval -1 ;
˜ ˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜^˜
mzROI.c:203:28: warning: implicit conversion changes signedness: 'const int' to 'unsigned int' [-Wsign-conversion]
mzval[i].scmax = scan;
˜ ^˜˜˜
mzROI.c:217:74: warning: implicit conversion changes signedness: 'unsigned int' to 'int' [-Wsign-conversion]
int lpos = lowerBound( fMass - ddev,scanbuf->nextScan,0,scanbuf->nextScanLength);
˜˜˜˜˜˜˜˜˜˜ ˜˜˜˜˜˜˜˜˜^˜˜˜˜˜˜˜˜˜˜˜˜˜
mzROI.c:218:92: warning: implicit conversion changes signedness: 'unsigned int' to 'int' [-Wsign-conversion]
int hpos = upperBound( fMass + ddev,scanbuf->nextScan,lpos,scanbuf->nextScanLength - lpos);
˜˜˜˜˜˜˜˜˜˜ ˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜^˜˜˜˜˜
mzROI.c:218:94: warning: implicit conversion changes signedness: 'int' to 'unsigned int' [-Wsign-conversion]
int hpos = upperBound( fMass + ddev,scanbuf->nextScan,lpos,scanbuf->nextScanLength - lpos);
˜ ^˜˜˜
mzROI.c:237:53: warning: implicit conversion changes signedness: 'unsigned int' to 'int' [-Wsign-conversion]
int i = lower_bound(fMass,mzval,0,mzLength->mzval);
˜˜˜˜˜˜˜˜˜˜˜ ˜˜˜˜˜˜˜˜˜˜^˜˜˜˜
mzROI.c:241:33: warning: implicit conversion changes signedness: 'unsigned int' to 'int' [-Wsign-conversion]
int n = mzLength->mzval - i;
˜ ˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜^˜˜
mzROI.c:241:35: warning: implicit conversion changes signedness: 'int' to 'unsigned int' [-Wsign-conversion]
int n = mzLength->mzval - i;
˜ ^
mzROI.c:244:46: warning: implicit conversion changes signedness: 'int' to 'unsigned long' [-Wsign-conversion]
memmove(mzval + i +1, mzval + i, n*sizeof(struct mzROIStruct));
^˜
/usr/include/secure/_string.h:63:42: note: expanded from macro 'memmove'
? __builtin___memmove_chk (dest, src, len, __darwin_obsz0 (dest)) \
^
mzROI.c:244:46: warning: implicit conversion changes signedness: 'int' to 'unsigned long' [-Wsign-conversion]
memmove(mzval + i +1, mzval + i, n*sizeof(struct mzROIStruct));
^˜
/usr/include/secure/_string.h:64:39: note: expanded from macro 'memmove'
: __inline_memmove_chk (dest, src, len))
^
mzROI.c:249:30: warning: implicit conversion turns floating-point number into integer: 'const double' to 'unsigned int' [-Wconversion]
mzval[i].intensity = fInten;
˜ ^˜˜˜˜˜
mzROI.c:250:26: warning: implicit conversion changes signedness: 'const int' to 'unsigned int' [-Wsign-conversion]
mzval[i].scmin = scan;
˜ ^˜˜˜
mzROI.c:251:26: warning: implicit conversion changes signedness: 'const int' to 'unsigned int' [-Wsign-conversion]
mzval[i].scmax = scan;
˜ ^˜˜˜
mzROI.c:279:26: warning: implicit conversion changes signedness: 'unsigned int' to 'int' [-Wsign-conversion]
p=mzLength->mzROI;
˜˜˜˜˜˜˜˜˜˜˜^˜˜˜˜
mzROI.c:280:46: warning: implicit conversion changes signedness: 'int' to 'unsigned int' [-Wsign-conversion]
mzROI=checkmzROIBufSize(mzROI, p+1 , mzLength);
˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜ ˜^˜
mzROI.c:319:80: warning: implicit conversion changes signedness: 'int' to 'unsigned int' [-Wsign-conversion]
struct mzROIStruct * tmp = (struct mzROIStruct *) calloc(mzLength->mzval - del, sizeof(struct mzROIStruct));
˜ ^˜˜
mzROI.c:321:106: warning: implicit conversion changes signedness: 'int' to 'unsigned int' [-Wsign-conversion]
error("findmzROI/cleanup: buffer memory could not be allocated ! (%d bytes)\n", (mzLength->mzval - del) * sizeof(struct mzROIStruct));
˜ ^˜˜
mzROI.c:349:23: warning: implicit conversion changes signedness: 'int' to 'unsigned int' [-Wsign-conversion]
mzLength->mzval = p;
˜ ^
mzROI.c:369:58: warning: implicit conversion changes signedness: 'int' to 'size_t' (aka 'unsigned long') [-Wsign-conversion]
scanbuf->thisScan= (struct scanStruct *) calloc(N, sizeof(struct scanStruct));
˜˜˜˜˜˜ ^
mzROI.c:374:33: warning: implicit conversion changes signedness: 'int' to 'unsigned int' [-Wsign-conversion]
scanbuf->thisScanLength=N;
˜^
mzROI.c:402:50: warning: implicit conversion changes signedness: 'int' to 'size_t' (aka 'unsigned long') [-Wsign-conversion]
scanbuf->nextScan= (double *) calloc(N, sizeof(double));
˜˜˜˜˜˜ ^
mzROI.c:405:37: warning: implicit conversion changes signedness: 'int' to 'unsigned int' [-Wsign-conversion]
scanbuf->nextScanLength=N;
˜^
mzROI.c:551:21: warning: implicit conversion loses floating-point precision: 'double' to 'float' [-Wconversion]
pickOptions.dev = REAL(dev)[0];
˜ ^˜˜˜˜˜˜˜˜˜˜˜
mzROI.c:552:28: warning: implicit conversion changes signedness: 'int' to 'unsigned int' [-Wsign-conversion]
pickOptions.minEntries = INTEGER(minEntries)[0];
˜ ^˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜
mzROI.c:553:32: warning: implicit conversion changes signedness: 'int' to 'unsigned int' [-Wsign-conversion]
pickOptions.minimumIntValues=INTEGER(prefilter)[0];
˜^˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜
mzROI.c:554:26: warning: implicit conversion changes signedness: 'int' to 'unsigned int' [-Wsign-conversion]
pickOptions.minimumInt=INTEGER(prefilter)[1];
˜^˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜
mzROI.c:645:45: warning: implicit conversion changes signedness: 'unsigned int' to 'int' [-Wsign-conversion]
INTEGER_POINTER(vscmin)[0] = mzROI[i].scmin;
˜ ˜˜˜˜˜˜˜˜˜^˜˜˜˜
mzROI.c:646:45: warning: implicit conversion changes signedness: 'unsigned int' to 'int' [-Wsign-conversion]
INTEGER_POINTER(vscmax)[0] = mzROI[i].scmax;
˜ ˜˜˜˜˜˜˜˜˜^˜˜˜˜
mzROI.c:647:46: warning: implicit conversion changes signedness: 'unsigned int' to 'int' [-Wsign-conversion]
INTEGER_POINTER(vlength)[0] = mzROI[i].length;
˜ ˜˜˜˜˜˜˜˜˜^˜˜˜˜˜
mzROI.c:648:49: warning: implicit conversion changes signedness: 'unsigned int' to 'int' [-Wsign-conversion]
INTEGER_POINTER(vintensity)[0] = mzROI[i].intensity;
˜ ˜˜˜˜˜˜˜˜˜^˜˜˜˜˜˜˜˜
36 warnings generated.
clang -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -I/usr/local/include -fPIC -mtune=native -g -O2 -Wall -pedantic -Wconversion -c util.c -o util.o
clang -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -I/usr/local/include -fPIC -mtune=native -g -O2 -Wall -pedantic -Wconversion -c xcms.c -o xcms.o
xcms.c:67:13: warning: implicit conversion turns floating-point number into integer: 'double' to 'int' [-Wconversion]
ibase = floor(*basespace/dx);
˜ ^˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜
xcms.c:72:13: warning: implicit conversion turns floating-point number into integer: 'double' to 'int' [-Wconversion]
ipost = round((xvals[ix] - *xstart)/dx);
˜ ^˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜
xcms.c:95:21: warning: implicit conversion turns floating-point number into integer: 'double' to 'int' [-Wconversion]
ipost = round((xvals[ix] - *xstart)/dx);
˜ ^˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜
xcms.c:276:53: warning: implicit conversion changes signedness: 'int' to 'unsigned long' [-Wsign-conversion]
double * sortBuf = (double *) malloc((*mrad*2+1)*(*nrad*2+1)*sizeof(double));
˜˜˜˜˜˜˜˜˜˜˜^˜˜˜˜˜˜˜˜˜˜˜˜
xcms.c:291:28: warning: implicit conversion changes signedness: 'int' to 'size_t' (aka 'unsigned long') [-Wsign-conversion]
qsort(sortBuf, bufLen, sizeof(double), CompareDouble);
˜˜˜˜˜ ^˜˜˜˜˜
5 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 xcms.so massifquant/xcms_massifquant.o massifquant/TrMgr.o massifquant/Tracker.o massifquant/SegProc.o massifquant/DataKeeper.o massifquant/OpOverload.o obiwarp/mat.o obiwarp/vec.o obiwarp/xcms_dynprog.o obiwarp/xcms_lmat.o xcms_obiwarp.o fastMatch.o mzClust_hclust.o mzROI.o util.o xcms.o -F/Library/Frameworks/R.framework/.. -framework R -Wl,-framework -Wl,CoreFoundation
installing to /Users/biocbuild/bbs-2.12-bioc/meat/xcms.buildbin-libdir/xcms/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 (xcms)
>>>>>>>
>>>>>>> FIXING LINKS FOR xcms.buildbin-libdir/xcms/libs//xcms.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" "xcms.buildbin-libdir/xcms/libs//xcms.so"
install_name_tool -change "/usr/local/lib/libgfortran.2.dylib" "/Library/Frameworks/R.framework/Versions/3.0/Resources/lib/libgfortran.2.dylib" "xcms.buildbin-libdir/xcms/libs//xcms.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" "xcms.buildbin-libdir/xcms/libs//xcms.so"
install_name_tool -change "/usr/local/lib/libreadline.dylib" "/Library/Frameworks/R.framework/Versions/3.0/Resources/lib/libreadline.dylib" "xcms.buildbin-libdir/xcms/libs//xcms.so"