>>>>>>>
>>>>>>> INSTALLATION WITH 'R CMD INSTALL --preclean --no-multiarch --library=Rdisop.buildbin-libdir Rdisop_1.20.0.tar.gz'
>>>>>>>
* installing *source* package 'Rdisop' ...
Makefile:1270: examples/.deps/peaklist.Po: No such file or directory
Makefile:1271: src/ims/.deps/alphabet.Plo: No such file or directory
Makefile:1272: src/ims/.deps/characteralphabet.Plo: No such file or directory
Makefile:1273: src/ims/.deps/composedelement.Plo: No such file or directory
Makefile:1274: src/ims/.deps/distributedalphabet.Plo: No such file or directory
Makefile:1275: src/ims/.deps/distributionprobabilityscorer.Plo: No such file or directory
Makefile:1276: src/ims/.deps/element.Plo: No such file or directory
Makefile:1277: src/ims/.deps/isotopedistribution.Plo: No such file or directory
Makefile:1278: src/ims/.deps/isotopespecies.Plo: No such file or directory
Makefile:1279: src/ims/.deps/nitrogenrulefilter.Plo: No such file or directory
Makefile:1280: src/ims/.deps/transformation.Plo: No such file or directory
Makefile:1281: src/ims/.deps/weights.Plo: No such file or directory
Makefile:1282: src/ims/base/parser/.deps/alphabettextparser.Plo: No such file or directory
Makefile:1283: src/ims/base/parser/.deps/distributedalphabettextparser.Plo: No such file or directory
Makefile:1284: src/ims/base/parser/.deps/keggligandcompoundsparser.Plo: No such file or directory
Makefile:1285: src/ims/base/parser/.deps/massestextparser.Plo: No such file or directory
Makefile:1286: src/ims/base/parser/.deps/moleculeionchargemodificationparser.Plo: No such file or directory
Makefile:1287: src/ims/base/parser/.deps/moleculesequenceparser.Plo: No such file or directory
Makefile:1288: src/ims/base/parser/.deps/standardmoleculesequenceparser.Plo: No such file or directory
Makefile:1289: src/ims/calib/.deps/linearpointsetmatcher.Plo: No such file or directory
Makefile:1290: src/ims/calib/.deps/linepairstabber.Plo: No such file or directory
Makefile:1291: src/ims/calib/.deps/matchmatrix.Plo: No such file or directory
Makefile:1292: src/ims/decomp/.deps/realmassdecomposer.Plo: No such file or directory
Makefile:1293: src/ims/utils/.deps/distribution.Plo: No such file or directory
Makefile:1294: tests/.deps/alphabettest.Po: No such file or directory
Makefile:1295: tests/.deps/chebyshevfittertest.Po: No such file or directory
Makefile:1296: tests/.deps/composedelementtest.Po: No such file or directory
Makefile:1297: tests/.deps/distributedalphabettest.Po: No such file or directory
Makefile:1298: tests/.deps/distributionprobabilityscorertest.Po: No such file or directory
Makefile:1299: tests/.deps/elementtest.Po: No such file or directory
Makefile:1300: tests/.deps/exceptiontest.Po: No such file or directory
Makefile:1301: tests/.deps/fragmentpeaktest.Po: No such file or directory
Makefile:1302: tests/.deps/identitytransformationtest.Po: No such file or directory
Makefile:1303: tests/.deps/intensitypeaktest.Po: No such file or directory
Makefile:1304: tests/.deps/isotopedistributiontest.Po: No such file or directory
Makefile:1305: tests/.deps/isotopespeciestest.Po: No such file or directory
Makefile:1306: tests/.deps/lineartransformationtest.Po: No such file or directory
Makefile:1307: tests/.deps/markovsequencegeneratortest.Po: No such file or directory
Makefile:1308: tests/.deps/massintensitypeaktest.Po: No such file or directory
Makefile:1309: tests/.deps/massintensitytofpeaktest.Po: No such file or directory
Makefile:1310: tests/.deps/masspeaktest.Po: No such file or directory
Makefile:1311: tests/.deps/masstofpeaktest.Po: No such file or directory
Makefile:1312: tests/.deps/peaklisttest.Po: No such file or directory
Makefile:1313: tests/.deps/peakpropertyiteratortest.Po: No such file or directory
Makefile:1314: tests/.deps/pmffragmentertest.Po: No such file or directory
Makefile:1315: tests/.deps/polynomialtransformationtest.Po: No such file or directory
Makefile:1316: tests/.deps/randomsequencegeneratortest.Po: No such file or directory
Makefile:1317: tests/.deps/roundtest.Po: No such file or directory
Makefile:1318: tests/.deps/shifttransformationtest.Po: No such file or directory
Makefile:1319: tests/.deps/stopwatchtest.Po: No such file or directory
Makefile:1320: tests/.deps/tests.Po: No such file or directory
Makefile:1321: tests/.deps/tofpeaktest.Po: No such file or directory
Makefile:1322: tests/.deps/weightstest.Po: No such file or directory
Makefile:1323: tests/base/parser/.deps/massestextparsertest.Po: No such file or directory
Makefile:1324: tests/base/parser/.deps/moleculesequenceparsertest.Po: No such file or directory
Makefile:1325: tests/calib/.deps/linearpointsetmatchertest.Po: No such file or directory
Makefile:1326: tests/calib/.deps/linepairstabbertest.Po: No such file or directory
Makefile:1327: tests/calib/.deps/matchmatrixtest.Po: No such file or directory
Makefile:1328: tests/decomp/.deps/integermassdecomposertest.Po: No such file or directory
Makefile:1329: tests/decomp/.deps/realmassdecomposertest.Po: No such file or directory
Makefile:1330: tests/decomp/.deps/twomassdecomposer2test.Po: No such file or directory
Makefile:1331: tests/modifier/.deps/intensitynormalizermodifiertest.Po: No such file or directory
Makefile:1332: tests/modifier/.deps/massrangemodifiertest.Po: No such file or directory
Makefile:1333: tests/modifier/.deps/multimodifiertest.Po: No such file or directory
Makefile:1334: tests/modifier/.deps/shiftmodifiertest.Po: No such file or directory
Makefile:1335: tests/modifier/.deps/sortmodifiertest.Po: No such file or directory
Makefile:1336: tests/modifier/.deps/unificationmodifiertest.Po: No such file or directory
Makefile:1337: tests/modifier/.deps/voidmodifiertest.Po: No such file or directory
Makefile:1338: tools/.deps/decompvalidation.Po: No such file or directory
Makefile:1339: tools/.deps/elementalcompositions.Po: No such file or directory
Makefile:1340: tools/.deps/histogram.Po: No such file or directory
Makefile:1341: tools/.deps/imsdecomp.Po: No such file or directory
Makefile:1342: tools/.deps/imsfrag.Po: No such file or directory
Makefile:1343: tools/.deps/imsintdecomp.Po: No such file or directory
Makefile:1344: tools/.deps/keggruntimes.Po: No such file or directory
Makefile:1345: tools/.deps/numberdecompositions.Po: No such file or directory
Makefile:1346: tools/.deps/options.Po: No such file or directory
Makefile:1347: tools/.deps/peaklistvalidation.Po: No such file or directory
Makefile:1348: tools/.deps/scoredecompositions.Po: No such file or directory
make: *** No rule to make target `tools/.deps/scoredecompositions.Po'.
make: *** No rule to make target `tools/.deps/peaklistvalidation.Po'.
make: *** No rule to make target `tools/.deps/options.Po'.
make: *** No rule to make target `tools/.deps/numberdecompositions.Po'.
make: *** No rule to make target `tools/.deps/keggruntimes.Po'.
make: *** No rule to make target `tools/.deps/imsintdecomp.Po'.
make: *** No rule to make target `tools/.deps/imsfrag.Po'.
make: *** No rule to make target `tools/.deps/imsdecomp.Po'.
make: *** No rule to make target `tools/.deps/histogram.Po'.
make: *** No rule to make target `tools/.deps/elementalcompositions.Po'.
make: *** No rule to make target `tools/.deps/decompvalidation.Po'.
make: *** No rule to make target `tests/modifier/.deps/voidmodifiertest.Po'.
make: *** No rule to make target `tests/modifier/.deps/unificationmodifiertest.Po'.
make: *** No rule to make target `tests/modifier/.deps/sortmodifiertest.Po'.
make: *** No rule to make target `tests/modifier/.deps/shiftmodifiertest.Po'.
make: *** No rule to make target `tests/modifier/.deps/multimodifiertest.Po'.
make: *** No rule to make target `tests/modifier/.deps/massrangemodifiertest.Po'.
make: *** No rule to make target `tests/modifier/.deps/intensitynormalizermodifiertest.Po'.
make: *** No rule to make target `tests/decomp/.deps/twomassdecomposer2test.Po'.
make: *** No rule to make target `tests/decomp/.deps/realmassdecomposertest.Po'.
make: *** No rule to make target `tests/decomp/.deps/integermassdecomposertest.Po'.
make: *** No rule to make target `tests/calib/.deps/matchmatrixtest.Po'.
make: *** No rule to make target `tests/calib/.deps/linepairstabbertest.Po'.
make: *** No rule to make target `tests/calib/.deps/linearpointsetmatchertest.Po'.
make: *** No rule to make target `tests/base/parser/.deps/moleculesequenceparsertest.Po'.
make: *** No rule to make target `tests/base/parser/.deps/massestextparsertest.Po'.
make: *** No rule to make target `tests/.deps/weightstest.Po'.
make: *** No rule to make target `tests/.deps/tofpeaktest.Po'.
make: *** No rule to make target `tests/.deps/tests.Po'.
make: *** No rule to make target `tests/.deps/stopwatchtest.Po'.
make: *** No rule to make target `tests/.deps/shifttransformationtest.Po'.
make: *** No rule to make target `tests/.deps/roundtest.Po'.
make: *** No rule to make target `tests/.deps/randomsequencegeneratortest.Po'.
make: *** No rule to make target `tests/.deps/polynomialtransformationtest.Po'.
make: *** No rule to make target `tests/.deps/pmffragmentertest.Po'.
make: *** No rule to make target `tests/.deps/peakpropertyiteratortest.Po'.
make: *** No rule to make target `tests/.deps/peaklisttest.Po'.
make: *** No rule to make target `tests/.deps/masstofpeaktest.Po'.
make: *** No rule to make target `tests/.deps/masspeaktest.Po'.
make: *** No rule to make target `tests/.deps/massintensitytofpeaktest.Po'.
make: *** No rule to make target `tests/.deps/massintensitypeaktest.Po'.
make: *** No rule to make target `tests/.deps/markovsequencegeneratortest.Po'.
make: *** No rule to make target `tests/.deps/lineartransformationtest.Po'.
make: *** No rule to make target `tests/.deps/isotopespeciestest.Po'.
make: *** No rule to make target `tests/.deps/isotopedistributiontest.Po'.
make: *** No rule to make target `tests/.deps/intensitypeaktest.Po'.
make: *** No rule to make target `tests/.deps/identitytransformationtest.Po'.
make: *** No rule to make target `tests/.deps/fragmentpeaktest.Po'.
make: *** No rule to make target `tests/.deps/exceptiontest.Po'.
make: *** No rule to make target `tests/.deps/elementtest.Po'.
make: *** No rule to make target `tests/.deps/distributionprobabilityscorertest.Po'.
make: *** No rule to make target `tests/.deps/distributedalphabettest.Po'.
make: *** No rule to make target `tests/.deps/composedelementtest.Po'.
make: *** No rule to make target `tests/.deps/chebyshevfittertest.Po'.
make: *** No rule to make target `tests/.deps/alphabettest.Po'.
make: *** No rule to make target `src/ims/utils/.deps/distribution.Plo'.
make: *** No rule to make target `src/ims/decomp/.deps/realmassdecomposer.Plo'.
make: *** No rule to make target `src/ims/calib/.deps/matchmatrix.Plo'.
make: *** No rule to make target `src/ims/calib/.deps/linepairstabber.Plo'.
make: *** No rule to make target `src/ims/calib/.deps/linearpointsetmatcher.Plo'.
make: *** No rule to make target `src/ims/base/parser/.deps/standardmoleculesequenceparser.Plo'.
make: *** No rule to make target `src/ims/base/parser/.deps/moleculesequenceparser.Plo'.
make: *** No rule to make target `src/ims/base/parser/.deps/moleculeionchargemodificationparser.Plo'.
make: *** No rule to make target `src/ims/base/parser/.deps/massestextparser.Plo'.
make: *** No rule to make target `src/ims/base/parser/.deps/keggligandcompoundsparser.Plo'.
make: *** No rule to make target `src/ims/base/parser/.deps/distributedalphabettextparser.Plo'.
make: *** No rule to make target `src/ims/base/parser/.deps/alphabettextparser.Plo'.
make: *** No rule to make target `src/ims/.deps/weights.Plo'.
make: *** No rule to make target `src/ims/.deps/transformation.Plo'.
make: *** No rule to make target `src/ims/.deps/nitrogenrulefilter.Plo'.
make: *** No rule to make target `src/ims/.deps/isotopespecies.Plo'.
make: *** No rule to make target `src/ims/.deps/isotopedistribution.Plo'.
make: *** No rule to make target `src/ims/.deps/element.Plo'.
make: *** No rule to make target `src/ims/.deps/distributionprobabilityscorer.Plo'.
make: *** No rule to make target `src/ims/.deps/distributedalphabet.Plo'.
make: *** No rule to make target `src/ims/.deps/composedelement.Plo'.
make: *** No rule to make target `src/ims/.deps/characteralphabet.Plo'.
make: *** No rule to make target `src/ims/.deps/alphabet.Plo'.
make: *** No rule to make target `examples/.deps/peaklist.Po'.
make: Failed to remake makefile `tools/.deps/scoredecompositions.Po'.
make: Failed to remake makefile `tools/.deps/peaklistvalidation.Po'.
make: Failed to remake makefile `tools/.deps/options.Po'.
make: Failed to remake makefile `tools/.deps/numberdecompositions.Po'.
make: Failed to remake makefile `tools/.deps/keggruntimes.Po'.
make: Failed to remake makefile `tools/.deps/imsintdecomp.Po'.
make: Failed to remake makefile `tools/.deps/imsfrag.Po'.
make: Failed to remake makefile `tools/.deps/imsdecomp.Po'.
make: Failed to remake makefile `tools/.deps/histogram.Po'.
make: Failed to remake makefile `tools/.deps/elementalcompositions.Po'.
make: Failed to remake makefile `tools/.deps/decompvalidation.Po'.
make: Failed to remake makefile `tests/modifier/.deps/voidmodifiertest.Po'.
make: Failed to remake makefile `tests/modifier/.deps/unificationmodifiertest.Po'.
make: Failed to remake makefile `tests/modifier/.deps/sortmodifiertest.Po'.
make: Failed to remake makefile `tests/modifier/.deps/shiftmodifiertest.Po'.
make: Failed to remake makefile `tests/modifier/.deps/multimodifiertest.Po'.
make: Failed to remake makefile `tests/modifier/.deps/massrangemodifiertest.Po'.
make: Failed to remake makefile `tests/modifier/.deps/intensitynormalizermodifiertest.Po'.
make: Failed to remake makefile `tests/decomp/.deps/twomassdecomposer2test.Po'.
make: Failed to remake makefile `tests/decomp/.deps/realmassdecomposertest.Po'.
make: Failed to remake makefile `tests/decomp/.deps/integermassdecomposertest.Po'.
make: Failed to remake makefile `tests/calib/.deps/matchmatrixtest.Po'.
make: Failed to remake makefile `tests/calib/.deps/linepairstabbertest.Po'.
make: Failed to remake makefile `tests/calib/.deps/linearpointsetmatchertest.Po'.
make: Failed to remake makefile `tests/base/parser/.deps/moleculesequenceparsertest.Po'.
make: Failed to remake makefile `tests/base/parser/.deps/massestextparsertest.Po'.
make: Failed to remake makefile `tests/.deps/weightstest.Po'.
make: Failed to remake makefile `tests/.deps/tofpeaktest.Po'.
make: Failed to remake makefile `tests/.deps/tests.Po'.
make: Failed to remake makefile `tests/.deps/stopwatchtest.Po'.
make: Failed to remake makefile `tests/.deps/shifttransformationtest.Po'.
make: Failed to remake makefile `tests/.deps/roundtest.Po'.
make: Failed to remake makefile `tests/.deps/randomsequencegeneratortest.Po'.
make: Failed to remake makefile `tests/.deps/polynomialtransformationtest.Po'.
make: Failed to remake makefile `tests/.deps/pmffragmentertest.Po'.
make: Failed to remake makefile `tests/.deps/peakpropertyiteratortest.Po'.
make: Failed to remake makefile `tests/.deps/peaklisttest.Po'.
make: Failed to remake makefile `tests/.deps/masstofpeaktest.Po'.
make: Failed to remake makefile `tests/.deps/masspeaktest.Po'.
make: Failed to remake makefile `tests/.deps/massintensitytofpeaktest.Po'.
make: Failed to remake makefile `tests/.deps/massintensitypeaktest.Po'.
make: Failed to remake makefile `tests/.deps/markovsequencegeneratortest.Po'.
make: Failed to remake makefile `tests/.deps/lineartransformationtest.Po'.
make: Failed to remake makefile `tests/.deps/isotopespeciestest.Po'.
make: Failed to remake makefile `tests/.deps/isotopedistributiontest.Po'.
make: Failed to remake makefile `tests/.deps/intensitypeaktest.Po'.
make: Failed to remake makefile `tests/.deps/identitytransformationtest.Po'.
make: Failed to remake makefile `tests/.deps/fragmentpeaktest.Po'.
make: Failed to remake makefile `tests/.deps/exceptiontest.Po'.
make: Failed to remake makefile `tests/.deps/elementtest.Po'.
make: Failed to remake makefile `tests/.deps/distributionprobabilityscorertest.Po'.
make: Failed to remake makefile `tests/.deps/distributedalphabettest.Po'.
make: Failed to remake makefile `tests/.deps/composedelementtest.Po'.
make: Failed to remake makefile `tests/.deps/chebyshevfittertest.Po'.
make: Failed to remake makefile `tests/.deps/alphabettest.Po'.
make: Failed to remake makefile `src/ims/utils/.deps/distribution.Plo'.
make: Failed to remake makefile `src/ims/decomp/.deps/realmassdecomposer.Plo'.
make: Failed to remake makefile `src/ims/calib/.deps/matchmatrix.Plo'.
make: Failed to remake makefile `src/ims/calib/.deps/linepairstabber.Plo'.
make: Failed to remake makefile `src/ims/calib/.deps/linearpointsetmatcher.Plo'.
make: Failed to remake makefile `src/ims/base/parser/.deps/standardmoleculesequenceparser.Plo'.
make: Failed to remake makefile `src/ims/base/parser/.deps/moleculesequenceparser.Plo'.
make: Failed to remake makefile `src/ims/base/parser/.deps/moleculeionchargemodificationparser.Plo'.
make: Failed to remake makefile `src/ims/base/parser/.deps/massestextparser.Plo'.
make: Failed to remake makefile `src/ims/base/parser/.deps/keggligandcompoundsparser.Plo'.
make: Failed to remake makefile `src/ims/base/parser/.deps/distributedalphabettextparser.Plo'.
make: Failed to remake makefile `src/ims/base/parser/.deps/alphabettextparser.Plo'.
make: Failed to remake makefile `src/ims/.deps/weights.Plo'.
make: Failed to remake makefile `src/ims/.deps/transformation.Plo'.
make: Failed to remake makefile `src/ims/.deps/nitrogenrulefilter.Plo'.
make: Failed to remake makefile `src/ims/.deps/isotopespecies.Plo'.
make: Failed to remake makefile `src/ims/.deps/isotopedistribution.Plo'.
make: Failed to remake makefile `src/ims/.deps/element.Plo'.
make: Failed to remake makefile `src/ims/.deps/distributionprobabilityscorer.Plo'.
make: Failed to remake makefile `src/ims/.deps/distributedalphabet.Plo'.
make: Failed to remake makefile `src/ims/.deps/composedelement.Plo'.
make: Failed to remake makefile `src/ims/.deps/characteralphabet.Plo'.
make: Failed to remake makefile `src/ims/.deps/alphabet.Plo'.
make: Failed to remake makefile `examples/.deps/peaklist.Po'.
rm -f tools/scoredecompositions tools/peaklistvalidation tools/numberdecompositions tools/keggruntimes tools/imsfrag tools/imsdecomp tools/imsintdecomp tools/histogram tools/decompvalidation tools/imsdecompstatic tools/elementalcompositions
test -z "src/libims.la" || rm -f src/libims.la
rm -f "src/so_locations"
rm -rf .libs _libs
rm -rf examples/.libs examples/_libs
rm -rf src/.libs src/_libs
rm -rf src/ims/.libs src/ims/_libs
rm -rf src/ims/base/parser/.libs src/ims/base/parser/_libs
rm -rf src/ims/calib/.libs src/ims/calib/_libs
rm -rf src/ims/decomp/.libs src/ims/decomp/_libs
rm -rf src/ims/utils/.libs src/ims/utils/_libs
rm -rf tests/.libs tests/_libs
rm -rf tools/.libs tools/_libs
rm -f *.o
rm -f examples/peaklist.o
rm -f src/ims/alphabet.o
rm -f src/ims/alphabet.lo
rm -f src/ims/base/parser/alphabettextparser.o
rm -f src/ims/base/parser/alphabettextparser.lo
rm -f src/ims/base/parser/distributedalphabettextparser.o
rm -f src/ims/base/parser/distributedalphabettextparser.lo
rm -f src/ims/base/parser/keggligandcompoundsparser.o
rm -f src/ims/base/parser/keggligandcompoundsparser.lo
rm -f src/ims/base/parser/massestextparser.o
rm -f src/ims/base/parser/massestextparser.lo
rm -f src/ims/base/parser/moleculeionchargemodificationparser.o
rm -f src/ims/base/parser/moleculeionchargemodificationparser.lo
rm -f src/ims/base/parser/moleculesequenceparser.o
rm -f src/ims/base/parser/moleculesequenceparser.lo
rm -f src/ims/base/parser/standardmoleculesequenceparser.o
rm -f src/ims/base/parser/standardmoleculesequenceparser.lo
rm -f src/ims/calib/linearpointsetmatcher.o
rm -f src/ims/calib/linearpointsetmatcher.lo
rm -f src/ims/calib/linepairstabber.o
rm -f src/ims/calib/linepairstabber.lo
rm -f src/ims/calib/matchmatrix.o
rm -f src/ims/calib/matchmatrix.lo
rm -f src/ims/characteralphabet.o
rm -f src/ims/characteralphabet.lo
rm -f src/ims/composedelement.o
rm -f src/ims/composedelement.lo
rm -f src/ims/decomp/realmassdecomposer.o
rm -f src/ims/decomp/realmassdecomposer.lo
rm -f src/ims/distributedalphabet.o
rm -f src/ims/distributedalphabet.lo
rm -f src/ims/distributionprobabilityscorer.o
rm -f src/ims/distributionprobabilityscorer.lo
rm -f src/ims/element.o
rm -f src/ims/element.lo
rm -f src/ims/isotopedistribution.o
rm -f src/ims/isotopedistribution.lo
rm -f src/ims/isotopespecies.o
rm -f src/ims/isotopespecies.lo
rm -f src/ims/nitrogenrulefilter.o
rm -f src/ims/nitrogenrulefilter.lo
rm -f src/ims/transformation.o
rm -f src/ims/transformation.lo
rm -f src/ims/utils/distribution.o
rm -f src/ims/utils/distribution.lo
rm -f src/ims/weights.o
rm -f src/ims/weights.lo
rm -f tests/alphabettest.o
rm -f tests/base/parser/massestextparsertest.o
rm -f tests/base/parser/moleculesequenceparsertest.o
rm -f tests/calib/linearpointsetmatchertest.o
rm -f tests/calib/linepairstabbertest.o
rm -f tests/calib/matchmatrixtest.o
rm -f tests/chebyshevfittertest.o
rm -f tests/composedelementtest.o
rm -f tests/decomp/integermassdecomposertest.o
rm -f tests/decomp/realmassdecomposertest.o
rm -f tests/decomp/twomassdecomposer2test.o
rm -f tests/distributedalphabettest.o
rm -f tests/distributionprobabilityscorertest.o
rm -f tests/elementtest.o
rm -f tests/exceptiontest.o
rm -f tests/fragmentpeaktest.o
rm -f tests/identitytransformationtest.o
rm -f tests/intensitypeaktest.o
rm -f tests/isotopedistributiontest.o
rm -f tests/isotopespeciestest.o
rm -f tests/lineartransformationtest.o
rm -f tests/markovsequencegeneratortest.o
rm -f tests/massintensitypeaktest.o
rm -f tests/massintensitytofpeaktest.o
rm -f tests/masspeaktest.o
rm -f tests/masstofpeaktest.o
rm -f tests/modifier/intensitynormalizermodifiertest.o
rm -f tests/modifier/massrangemodifiertest.o
rm -f tests/modifier/multimodifiertest.o
rm -f tests/modifier/shiftmodifiertest.o
rm -f tests/modifier/sortmodifiertest.o
rm -f tests/modifier/unificationmodifiertest.o
rm -f tests/modifier/voidmodifiertest.o
rm -f tests/peaklisttest.o
rm -f tests/peakpropertyiteratortest.o
rm -f tests/pmffragmentertest.o
rm -f tests/polynomialtransformationtest.o
rm -f tests/randomsequencegeneratortest.o
rm -f tests/roundtest.o
rm -f tests/shifttransformationtest.o
rm -f tests/stopwatchtest.o
rm -f tests/tests.o
rm -f tests/tofpeaktest.o
rm -f tests/weightstest.o
rm -f tools/decompvalidation.o
rm -f tools/elementalcompositions.o
rm -f tools/histogram.o
rm -f tools/imsdecomp.o
rm -f tools/imsfrag.o
rm -f tools/imsintdecomp.o
rm -f tools/keggruntimes.o
rm -f tools/numberdecompositions.o
rm -f tools/options.o
rm -f tools/peaklistvalidation.o
rm -f tools/scoredecompositions.o
rm -f *.lo
** libs
clang++ -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -I/usr/local/include -I"/Library/Frameworks/R.framework/Versions/3.0/Resources/library/RcppClassic/include" -I"/Library/Frameworks/R.framework/Versions/3.0/Resources/library/Rcpp/include" -I./imslib/src/ -fPIC -mtune=native -g -O2 -Wall -pedantic -Wconversion -c disop.cpp -o disop.o
In file included from disop.cpp:18:
In file included from ./imslib/src/ims/alphabet.h:8:
./imslib/src/ims/element.h:169:35: warning: implicit conversion changes signedness: 'int' to 'size_type' (aka 'unsigned long') [-Wsign-conversion]
if (isotopes.getAbundance(i) > 0.5) {
˜˜˜˜˜˜˜˜ ^
./imslib/src/ims/element.h:175:28: warning: implicit conversion changes signedness: 'int' to 'size_type' (aka 'unsigned long') [-Wsign-conversion]
return isotopes.getMass(i);
˜˜˜˜˜˜˜˜ ^
./imslib/src/ims/element.h:177:35: warning: implicit conversion changes signedness: 'int' to 'size_type' (aka 'unsigned long') [-Wsign-conversion]
if (isotopes.getAbundance(i) > maxval) {
˜˜˜˜˜˜˜˜ ^
./imslib/src/ims/element.h:178:35: warning: implicit conversion changes signedness: 'int' to 'size_type' (aka 'unsigned long') [-Wsign-conversion]
maxval = isotopes.getAbundance(i);
˜˜˜˜˜˜˜˜ ^
./imslib/src/ims/element.h:183:31: warning: implicit conversion changes signedness: 'int' to 'size_type' (aka 'unsigned long') [-Wsign-conversion]
return isotopes.getMass(maxindex);
˜˜˜˜˜˜˜˜ ^˜˜˜˜˜˜˜
In file included from disop.cpp:26:
./imslib/src/ims/decomp/realmassdecomposer.h:55:20: warning: 'long long' is a C++11 extension [-Wc++11-long-long]
typedef unsigned long long number_of_decompositions_type;
^
In file included from disop.cpp:33:
In file included from /Library/Frameworks/R.framework/Versions/3.0/Resources/library/RcppClassic/include/RcppClassic.h:27:
In file included from /Library/Frameworks/R.framework/Versions/3.0/Resources/library/Rcpp/include/RcppCommon.h:117:
/Library/Frameworks/R.framework/Versions/3.0/Resources/library/Rcpp/include/Rcpp/internal/wrap.h:130:17: warning: implicit conversion changes signedness: 'int' to 'unsigned long' [-Wsign-conversion]
switch (size - i){
˜ ^
/Library/Frameworks/R.framework/Versions/3.0/Resources/library/Rcpp/include/Rcpp/internal/wrap.h:190:44: warning: implicit conversion changes signedness: 'size_t' (aka 'unsigned long') to 'R_xlen_t' (aka 'long') [-Wsign-conversion]
SEXP x = PROTECT( Rf_allocVector( VECSXP, size ) );
˜˜˜˜˜˜˜˜˜˜˜˜˜˜ ^˜˜˜
/Library/Frameworks/R.framework/Resources/include/Rinternals.h:547:31: note: expanded from macro 'PROTECT'
#define PROTECT(s) Rf_protect(s)
^
In file included from disop.cpp:33:
In file included from /Library/Frameworks/R.framework/Versions/3.0/Resources/library/RcppClassic/include/RcppClassic.h:27:
In file included from /Library/Frameworks/R.framework/Versions/3.0/Resources/library/Rcpp/include/RcppCommon.h:117:
/Library/Frameworks/R.framework/Versions/3.0/Resources/library/Rcpp/include/Rcpp/internal/wrap.h:209:44: warning: implicit conversion changes signedness: 'size_t' (aka 'unsigned long') to 'R_xlen_t' (aka 'long') [-Wsign-conversion]
SEXP x = PROTECT( Rf_allocVector( STRSXP, size ) ) ;
˜˜˜˜˜˜˜˜˜˜˜˜˜˜ ^˜˜˜
/Library/Frameworks/R.framework/Resources/include/Rinternals.h:547:31: note: expanded from macro 'PROTECT'
#define PROTECT(s) Rf_protect(s)
^
In file included from disop.cpp:33:
In file included from /Library/Frameworks/R.framework/Versions/3.0/Resources/library/RcppClassic/include/RcppClassic.h:27:
In file included from /Library/Frameworks/R.framework/Versions/3.0/Resources/library/Rcpp/include/RcppCommon.h:117:
/Library/Frameworks/R.framework/Versions/3.0/Resources/library/Rcpp/include/Rcpp/internal/wrap.h:237:48: warning: implicit conversion changes signedness: 'size_t' (aka 'unsigned long') to 'R_xlen_t' (aka 'long') [-Wsign-conversion]
SEXP names = PROTECT( Rf_allocVector( STRSXP, size ) ) ;
˜˜˜˜˜˜˜˜˜˜˜˜˜˜ ^˜˜˜
/Library/Frameworks/R.framework/Resources/include/Rinternals.h:547:31: note: expanded from macro 'PROTECT'
#define PROTECT(s) Rf_protect(s)
^
In file included from disop.cpp:33:
In file included from /Library/Frameworks/R.framework/Versions/3.0/Resources/library/RcppClassic/include/RcppClassic.h:27:
In file included from /Library/Frameworks/R.framework/Versions/3.0/Resources/library/Rcpp/include/RcppCommon.h:117:
/Library/Frameworks/R.framework/Versions/3.0/Resources/library/Rcpp/include/Rcpp/internal/wrap.h:245:26: warning: implicit conversion changes signedness: 'size_t' (aka 'unsigned long') to 'R_xlen_t' (aka 'long') [-Wsign-conversion]
SET_STRING_ELT( names, i, Rf_mkChar(buf.c_str()) ) ;
˜˜˜˜˜˜˜˜˜˜˜˜˜˜ ^
/Library/Frameworks/R.framework/Versions/3.0/Resources/library/Rcpp/include/Rcpp/internal/wrap.h:266:48: warning: implicit conversion changes signedness: 'size_t' (aka 'unsigned long') to 'R_xlen_t' (aka 'long') [-Wsign-conversion]
SEXP names = PROTECT( Rf_allocVector( STRSXP, size ) ) ;
˜˜˜˜˜˜˜˜˜˜˜˜˜˜ ^˜˜˜
/Library/Frameworks/R.framework/Resources/include/Rinternals.h:547:31: note: expanded from macro 'PROTECT'
#define PROTECT(s) Rf_protect(s)
^
In file included from disop.cpp:33:
In file included from /Library/Frameworks/R.framework/Versions/3.0/Resources/library/RcppClassic/include/RcppClassic.h:27:
In file included from /Library/Frameworks/R.framework/Versions/3.0/Resources/library/Rcpp/include/RcppCommon.h:117:
/Library/Frameworks/R.framework/Versions/3.0/Resources/library/Rcpp/include/Rcpp/internal/wrap.h:274:26: warning: implicit conversion changes signedness: 'size_t' (aka 'unsigned long') to 'R_xlen_t' (aka 'long') [-Wsign-conversion]
SET_STRING_ELT( names, i, Rf_mkChar(buf.c_str()) ) ;
˜˜˜˜˜˜˜˜˜˜˜˜˜˜ ^
/Library/Frameworks/R.framework/Versions/3.0/Resources/library/Rcpp/include/Rcpp/internal/wrap.h:311:44: warning: implicit conversion changes signedness: 'size_t' (aka 'unsigned long') to 'R_xlen_t' (aka 'long') [-Wsign-conversion]
SEXP x = PROTECT( Rf_allocVector( VECSXP, size ) );
˜˜˜˜˜˜˜˜˜˜˜˜˜˜ ^˜˜˜
/Library/Frameworks/R.framework/Resources/include/Rinternals.h:547:31: note: expanded from macro 'PROTECT'
#define PROTECT(s) Rf_protect(s)
^
In file included from disop.cpp:33:
In file included from /Library/Frameworks/R.framework/Versions/3.0/Resources/library/RcppClassic/include/RcppClassic.h:27:
In file included from /Library/Frameworks/R.framework/Versions/3.0/Resources/library/Rcpp/include/RcppCommon.h:117:
/Library/Frameworks/R.framework/Versions/3.0/Resources/library/Rcpp/include/Rcpp/internal/wrap.h:312:48: warning: implicit conversion changes signedness: 'size_t' (aka 'unsigned long') to 'R_xlen_t' (aka 'long') [-Wsign-conversion]
SEXP names = PROTECT( Rf_allocVector( STRSXP, size ) ) ;
˜˜˜˜˜˜˜˜˜˜˜˜˜˜ ^˜˜˜
/Library/Frameworks/R.framework/Resources/include/Rinternals.h:547:31: note: expanded from macro 'PROTECT'
#define PROTECT(s) Rf_protect(s)
^
In file included from disop.cpp:33:
In file included from /Library/Frameworks/R.framework/Versions/3.0/Resources/library/RcppClassic/include/RcppClassic.h:27:
In file included from /Library/Frameworks/R.framework/Versions/3.0/Resources/library/Rcpp/include/RcppCommon.h:117:
/Library/Frameworks/R.framework/Versions/3.0/Resources/library/Rcpp/include/Rcpp/internal/wrap.h:319:22: warning: implicit conversion changes signedness: 'size_t' (aka 'unsigned long') to 'R_xlen_t' (aka 'long') [-Wsign-conversion]
SET_VECTOR_ELT( x, i, element ) ;
˜˜˜˜˜˜˜˜˜˜˜˜˜˜ ^
/Library/Frameworks/R.framework/Versions/3.0/Resources/library/Rcpp/include/Rcpp/internal/wrap.h:320:26: warning: implicit conversion changes signedness: 'size_t' (aka 'unsigned long') to 'R_xlen_t' (aka 'long') [-Wsign-conversion]
SET_STRING_ELT( names, i, Rf_mkChar(buf.c_str()) ) ;
˜˜˜˜˜˜˜˜˜˜˜˜˜˜ ^
/Library/Frameworks/R.framework/Versions/3.0/Resources/library/Rcpp/include/Rcpp/internal/wrap.h:343:44: warning: implicit conversion changes signedness: 'size_t' (aka 'unsigned long') to 'R_xlen_t' (aka 'long') [-Wsign-conversion]
SEXP x = PROTECT( Rf_allocVector( STRSXP, size ) ) ;
˜˜˜˜˜˜˜˜˜˜˜˜˜˜ ^˜˜˜
/Library/Frameworks/R.framework/Resources/include/Rinternals.h:547:31: note: expanded from macro 'PROTECT'
#define PROTECT(s) Rf_protect(s)
^
In file included from disop.cpp:33:
In file included from /Library/Frameworks/R.framework/Versions/3.0/Resources/library/RcppClassic/include/RcppClassic.h:27:
In file included from /Library/Frameworks/R.framework/Versions/3.0/Resources/library/Rcpp/include/RcppCommon.h:117:
/Library/Frameworks/R.framework/Versions/3.0/Resources/library/Rcpp/include/Rcpp/internal/wrap.h:344:48: warning: implicit conversion changes signedness: 'size_t' (aka 'unsigned long') to 'R_xlen_t' (aka 'long') [-Wsign-conversion]
SEXP names = PROTECT( Rf_allocVector( STRSXP, size ) ) ;
˜˜˜˜˜˜˜˜˜˜˜˜˜˜ ^˜˜˜
/Library/Frameworks/R.framework/Resources/include/Rinternals.h:547:31: note: expanded from macro 'PROTECT'
#define PROTECT(s) Rf_protect(s)
^
In file included from disop.cpp:33:
In file included from /Library/Frameworks/R.framework/Versions/3.0/Resources/library/RcppClassic/include/RcppClassic.h:27:
In file included from /Library/Frameworks/R.framework/Versions/3.0/Resources/library/Rcpp/include/RcppCommon.h:117:
/Library/Frameworks/R.framework/Versions/3.0/Resources/library/Rcpp/include/Rcpp/internal/wrap.h:484:44: warning: implicit conversion changes signedness: 'size_t' (aka 'unsigned long') to 'R_xlen_t' (aka 'long') [-Wsign-conversion]
SEXP x = PROTECT( Rf_allocVector( LGLSXP, size ) );
˜˜˜˜˜˜˜˜˜˜˜˜˜˜ ^˜˜˜
/Library/Frameworks/R.framework/Resources/include/Rinternals.h:547:31: note: expanded from macro 'PROTECT'
#define PROTECT(s) Rf_protect(s)
^
In file included from disop.cpp:33:
In file included from /Library/Frameworks/R.framework/Versions/3.0/Resources/library/RcppClassic/include/RcppClassic.h:29:
In file included from /Library/Frameworks/R.framework/Versions/3.0/Resources/library/Rcpp/include/Rcpp.h:50:
/Library/Frameworks/R.framework/Versions/3.0/Resources/library/Rcpp/include/Rcpp/Language.h:173:76: warning: implicit conversion changes signedness: 'int' to 'const size_t' (aka 'const unsigned long') [-Wsign-conversion]
unary_call( Language call_, int index ) : call(call_), proxy(call_,index){}
˜˜˜˜˜ ^˜˜˜˜
/Library/Frameworks/R.framework/Versions/3.0/Resources/library/Rcpp/include/Rcpp/Language.h:190:91: warning: implicit conversion changes signedness: 'int' to 'const size_t' (aka 'const unsigned long') [-Wsign-conversion]
binary_call( Language call_, int index1, int index2 ) : call(call_), proxy1(call_,index1), proxy2(call_,index2){}
˜˜˜˜˜˜ ^˜˜˜˜˜
/Library/Frameworks/R.framework/Versions/3.0/Resources/library/Rcpp/include/Rcpp/Language.h:190:113: warning: implicit conversion changes signedness: 'int' to 'const size_t' (aka 'const unsigned long') [-Wsign-conversion]
binary_call( Language call_, int index1, int index2 ) : call(call_), proxy1(call_,index1), proxy2(call_,index2){}
˜˜˜˜˜˜ ^˜˜˜˜˜
In file included from disop.cpp:33:
In file included from /Library/Frameworks/R.framework/Versions/3.0/Resources/library/RcppClassic/include/RcppClassic.h:29:
In file included from /Library/Frameworks/R.framework/Versions/3.0/Resources/library/Rcpp/include/Rcpp.h:60:
/Library/Frameworks/R.framework/Versions/3.0/Resources/library/Rcpp/include/Rcpp/Datetime.h:40:40: warning: implicit conversion changes signedness: 'const unsigned int' to 'int' [-Wsign-conversion]
int getMicroSeconds() const { return m_us; }
˜˜˜˜˜˜ ^˜˜˜
In file included from disop.cpp:33:
In file included from /Library/Frameworks/R.framework/Versions/3.0/Resources/library/RcppClassic/include/RcppClassic.h:29:
In file included from /Library/Frameworks/R.framework/Versions/3.0/Resources/library/Rcpp/include/Rcpp.h:70:
In file included from /Library/Frameworks/R.framework/Versions/3.0/Resources/library/Rcpp/include/Rcpp/sugar/sugar.h:28:
In file included from /Library/Frameworks/R.framework/Versions/3.0/Resources/library/Rcpp/include/Rcpp/hash/hash.h:27:
/Library/Frameworks/R.framework/Versions/3.0/Resources/library/Rcpp/include/Rcpp/hash/IndexHash.h:197:16: warning: implicit conversion changes signedness: 'unsigned int' to 'int' [-Wsign-conversion]
return RCPP_HASH(value) ;
˜˜˜˜˜˜ ^˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜
/Library/Frameworks/R.framework/Versions/3.0/Resources/library/Rcpp/include/Rcpp/hash/IndexHash.h:45:61: note: expanded from macro 'RCPP_HASH'
#define RCPP_HASH(X) (3141592653U * ((unsigned int)(X)) >> (32 - k))
˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜^˜˜˜˜˜˜˜˜˜˜
/Library/Frameworks/R.framework/Versions/3.0/Resources/library/Rcpp/include/Rcpp/hash/IndexHash.h:212:14: warning: implicit conversion changes signedness: 'unsigned int' to 'int' [-Wsign-conversion]
addr = RCPP_HASH(val_u.u[0] + val_u.u[1]);
˜ ^˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜
/Library/Frameworks/R.framework/Versions/3.0/Resources/library/Rcpp/include/Rcpp/hash/IndexHash.h:45:61: note: expanded from macro 'RCPP_HASH'
#define RCPP_HASH(X) (3141592653U * ((unsigned int)(X)) >> (32 - k))
˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜^˜˜˜˜˜˜˜˜˜˜
/Library/Frameworks/R.framework/Versions/3.0/Resources/library/Rcpp/include/Rcpp/hash/IndexHash.h:221:18: warning: implicit conversion changes signedness: 'unsigned int' to 'int' [-Wsign-conversion]
addr = RCPP_HASH((val & 0xffffffff) ^ (val >> 32));
˜ ^˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜
/Library/Frameworks/R.framework/Versions/3.0/Resources/library/Rcpp/include/Rcpp/hash/IndexHash.h:45:61: note: expanded from macro 'RCPP_HASH'
#define RCPP_HASH(X) (3141592653U * ((unsigned int)(X)) >> (32 - k))
˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜^˜˜˜˜˜˜˜˜˜˜
In file included from disop.cpp:33:
In file included from /Library/Frameworks/R.framework/Versions/3.0/Resources/library/RcppClassic/include/RcppClassic.h:29:
In file included from /Library/Frameworks/R.framework/Versions/3.0/Resources/library/Rcpp/include/Rcpp.h:70:
In file included from /Library/Frameworks/R.framework/Versions/3.0/Resources/library/Rcpp/include/Rcpp/sugar/sugar.h:28:
In file included from /Library/Frameworks/R.framework/Versions/3.0/Resources/library/Rcpp/include/Rcpp/hash/hash.h:28:
/Library/Frameworks/R.framework/Versions/3.0/Resources/library/Rcpp/include/Rcpp/hash/SelfHash.h:95:16: warning: implicit conversion changes signedness: 'unsigned int' to 'int' [-Wsign-conversion]
return RCPP_HASH(value) ;
˜˜˜˜˜˜ ^˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜
/Library/Frameworks/R.framework/Versions/3.0/Resources/library/Rcpp/include/Rcpp/hash/IndexHash.h:45:61: note: expanded from macro 'RCPP_HASH'
#define RCPP_HASH(X) (3141592653U * ((unsigned int)(X)) >> (32 - k))
˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜^˜˜˜˜˜˜˜˜˜˜
In file included from disop.cpp:33:
In file included from /Library/Frameworks/R.framework/Versions/3.0/Resources/library/RcppClassic/include/RcppClassic.h:29:
In file included from /Library/Frameworks/R.framework/Versions/3.0/Resources/library/Rcpp/include/Rcpp.h:70:
In file included from /Library/Frameworks/R.framework/Versions/3.0/Resources/library/Rcpp/include/Rcpp/sugar/sugar.h:28:
In file included from /Library/Frameworks/R.framework/Versions/3.0/Resources/library/Rcpp/include/Rcpp/hash/hash.h:28:
/Library/Frameworks/R.framework/Versions/3.0/Resources/library/Rcpp/include/Rcpp/hash/SelfHash.h:110:14: warning: implicit conversion changes signedness: 'unsigned int' to 'int' [-Wsign-conversion]
addr = RCPP_HASH(val_u.u[0] + val_u.u[1]);
˜ ^˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜
/Library/Frameworks/R.framework/Versions/3.0/Resources/library/Rcpp/include/Rcpp/hash/IndexHash.h:45:61: note: expanded from macro 'RCPP_HASH'
#define RCPP_HASH(X) (3141592653U * ((unsigned int)(X)) >> (32 - k))
˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜^˜˜˜˜˜˜˜˜˜˜
In file included from disop.cpp:33:
In file included from /Library/Frameworks/R.framework/Versions/3.0/Resources/library/RcppClassic/include/RcppClassic.h:29:
In file included from /Library/Frameworks/R.framework/Versions/3.0/Resources/library/Rcpp/include/Rcpp.h:70:
In file included from /Library/Frameworks/R.framework/Versions/3.0/Resources/library/Rcpp/include/Rcpp/sugar/sugar.h:28:
In file included from /Library/Frameworks/R.framework/Versions/3.0/Resources/library/Rcpp/include/Rcpp/hash/hash.h:28:
/Library/Frameworks/R.framework/Versions/3.0/Resources/library/Rcpp/include/Rcpp/hash/SelfHash.h:119:18: warning: implicit conversion changes signedness: 'unsigned int' to 'int' [-Wsign-conversion]
addr = RCPP_HASH((val & 0xffffffff) ^ (val >> 32));
˜ ^˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜
/Library/Frameworks/R.framework/Versions/3.0/Resources/library/Rcpp/include/Rcpp/hash/IndexHash.h:45:61: note: expanded from macro 'RCPP_HASH'
#define RCPP_HASH(X) (3141592653U * ((unsigned int)(X)) >> (32 - k))
˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜^˜˜˜˜˜˜˜˜˜˜
In file included from disop.cpp:33:
In file included from /Library/Frameworks/R.framework/Versions/3.0/Resources/library/RcppClassic/include/RcppClassic.h:29:
In file included from /Library/Frameworks/R.framework/Versions/3.0/Resources/library/Rcpp/include/Rcpp.h:70:
In file included from /Library/Frameworks/R.framework/Versions/3.0/Resources/library/Rcpp/include/Rcpp/sugar/sugar.h:31:
In file included from /Library/Frameworks/R.framework/Versions/3.0/Resources/library/Rcpp/include/Rcpp/sugar/functions/functions.h:37:
/Library/Frameworks/R.framework/Versions/3.0/Resources/library/Rcpp/include/Rcpp/sugar/functions/seq_along.h:49:24: warning: implicit conversion loses integer precision: 'const size_t' (aka 'const unsigned long') to 'int' [-Wshorten-64-to-32]
return sugar::SeqLen( n ) ;
˜˜˜˜˜ ^
disop.cpp:76:4: warning: implicit conversion loses floating-point precision: 'double' to 'float' [-Wconversion]
+ 0.5 * (static_cast<int>(molecule.getElementAbundance("N"))
^˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜
disop.cpp:106:8: warning: unused variable 'parityeven' [-Wunused-variable]
bool parityeven = !parityodd;
^
disop.cpp:308:39: warning: implicit conversion changes signedness: 'distribution_t::size_type' (aka 'unsigned long') to 'const difference_type' (aka 'const long') [-Wsign-conversion]
candidate_abundances.begin() + size,
˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜ ^˜˜˜
disop.cpp:313:37: warning: implicit conversion changes signedness: 'distribution_t::size_type' (aka 'unsigned long') to 'const difference_type' (aka 'const long') [-Wsign-conversion]
candidate_abundances.begin() + size, // end of source range
˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜ ^˜˜˜
disop.cpp:181:6: warning: unused variable 'number_molecules_shown' [-Wunused-variable]
int number_molecules_shown = 100;
^
disop.cpp:219:32: warning: implicit conversion loses integer precision: 'peaks_container::size_type' (aka 'unsigned long') to 'int' [-Wshorten-64-to-32]
abundances_sum += abundances(i);
˜˜˜˜˜˜˜˜˜˜ ^
disop.cpp:222:14: warning: implicit conversion loses integer precision: 'peaks_container::size_type' (aka 'unsigned long') to 'int' [-Wshorten-64-to-32]
abundances(i) /= abundances_sum;
˜˜˜˜˜˜˜˜˜˜ ^
disop.cpp:230:36: warning: implicit conversion loses integer precision: 'masses_container::size_type' (aka 'unsigned long') to 'int' [-Wshorten-64-to-32]
peaklist_masses.push_back(masses(mi));
˜˜˜˜˜˜ ^˜
disop.cpp:231:44: warning: implicit conversion loses integer precision: 'masses_container::size_type' (aka 'unsigned long') to 'int' [-Wshorten-64-to-32]
peaklist_abundances.push_back(abundances(mi));
˜˜˜˜˜˜˜˜˜˜ ^˜
disop.cpp:380:36: warning: implicit conversion loses integer precision: 'masses_container::size_type' (aka 'unsigned long') to 'int' [-Wshorten-64-to-32]
peaklist_masses.push_back(masses(mi));
˜˜˜˜˜˜ ^˜
disop.cpp:381:44: warning: implicit conversion loses integer precision: 'masses_container::size_type' (aka 'unsigned long') to 'int' [-Wshorten-64-to-32]
peaklist_abundances.push_back(abundances(mi));
˜˜˜˜˜˜˜˜˜˜ ^˜
disop.cpp:396:32: warning: implicit conversion loses integer precision: 'peaks_container::size_type' (aka 'unsigned long') to 'int' [-Wshorten-64-to-32]
abundances_sum += abundances(i);
˜˜˜˜˜˜˜˜˜˜ ^
disop.cpp:399:14: warning: implicit conversion loses integer precision: 'peaks_container::size_type' (aka 'unsigned long') to 'int' [-Wshorten-64-to-32]
abundances(i) /= abundances_sum;
˜˜˜˜˜˜˜˜˜˜ ^
disop.cpp:404:32: warning: implicit conversion loses integer precision: 'masses_container::size_type' (aka 'unsigned long') to 'int' [-Wshorten-64-to-32]
mess_masses.push_back(masses(mi));
˜˜˜˜˜˜ ^˜
disop.cpp:405:40: warning: implicit conversion loses integer precision: 'masses_container::size_type' (aka 'unsigned long') to 'int' [-Wshorten-64-to-32]
mess_abundances.push_back(abundances(mi));
˜˜˜˜˜˜˜˜˜˜ ^˜
disop.cpp:652:16: warning: implicit conversion changes signedness: 'unsigned int' to 'int' [-Wsign-conversion]
charge(i) = z;
˜˜˜˜˜˜ ^
disop.cpp:669:44: warning: implicit conversion changes signedness: 'int' to 'size_type' (aka 'unsigned long') [-Wsign-conversion]
REAL(tmp_isotopes)[0 + 2*j] = masses[j];
˜˜˜˜˜˜ ^
disop.cpp:670:49: warning: implicit conversion changes signedness: 'int' to 'size_type' (aka 'unsigned long') [-Wsign-conversion]
REAL(tmp_isotopes)[1 + 2*j] = intensities[j];
˜˜˜˜˜˜˜˜˜˜˜ ^
disop.cpp:714:25: warning: implicit conversion changes signedness: 'const int' to 'size_type' (aka 'unsigned long') [-Wsign-conversion]
distribution_t::SIZE = maxisotopes;
˜ ^˜˜˜˜˜˜˜˜˜˜
disop.cpp:819:26: warning: implicit conversion changes signedness: 'const int' to 'size_type' (aka 'unsigned long') [-Wsign-conversion]
distribution_t::SIZE = maxisotopes;
˜ ^˜˜˜˜˜˜˜˜˜˜
disop.cpp:825:59: warning: conversion from string literal to 'char *' is deprecated [-Wdeprecated-writable-strings]
const char *symbol = CHAR(Rf_asChar(getListElement(l, "name")));
^
/Library/Frameworks/R.framework/Resources/include/Rinternals.h:395:25: note: expanded from macro 'CHAR'
#define CHAR(x) R_CHAR(x)
^
disop.cpp:827:80: warning: conversion from string literal to 'char *' is deprecated [-Wdeprecated-writable-strings]
nominal_mass_type nominalmass = (nominal_mass_type) REAL(getListElement(l, "mass"))[0];
^
disop.cpp:829:38: warning: conversion from string literal to 'char *' is deprecated [-Wdeprecated-writable-strings]
SEXP isotope = getListElement(l, "isotope");
^
disop.cpp:831:57: warning: conversion from string literal to 'char *' is deprecated [-Wdeprecated-writable-strings]
int numisotopes = Rf_length(getListElement(isotope, "mass"));
^
disop.cpp:832:49: warning: conversion from string literal to 'char *' is deprecated [-Wdeprecated-writable-strings]
double *mass = REAL(getListElement(isotope, "mass"));
^
disop.cpp:833:54: warning: conversion from string literal to 'char *' is deprecated [-Wdeprecated-writable-strings]
double *abundance = REAL(getListElement(isotope, "abundance"));
^
In file included from disop.cpp:33:
In file included from /Library/Frameworks/R.framework/Versions/3.0/Resources/library/RcppClassic/include/RcppClassic.h:27:
In file included from /Library/Frameworks/R.framework/Versions/3.0/Resources/library/Rcpp/include/RcppCommon.h:117:
/Library/Frameworks/R.framework/Versions/3.0/Resources/library/Rcpp/include/Rcpp/internal/wrap.h:104:16: warning: implicit conversion changes signedness: 'typename iterator_traits<__normal_iterator<const Date *, vector<Date, allocator<Date> > > >::difference_type' (aka 'long') to 'size_t' (aka 'unsigned long') [-Wsign-conversion]
size_t size = std::distance( first, last ) ;
˜˜˜˜ ^˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜
/Library/Frameworks/R.framework/Versions/3.0/Resources/library/Rcpp/include/Rcpp/internal/wrap.h:178:9: note: in instantiation of function template specialization 'Rcpp::internal::primitive_range_wrap__impl<__gnu_cxx::__normal_iterator<const Rcpp::Date *, std::vector<Rcpp::Date, std::allocator<Rcpp::Date> > >, Rcpp::Date>' requested here
return primitive_range_wrap__impl<InputIterator,T>( first, last, typename ::Rcpp::traits::r_sexptype_needscast<T>() ) ;
^
/Library/Frameworks/R.framework/Versions/3.0/Resources/library/Rcpp/include/Rcpp/internal/wrap.h:364:9: note: in instantiation of function template specialization 'Rcpp::internal::range_wrap_dispatch___impl<__gnu_cxx::__normal_iterator<const Rcpp::Date *, std::vector<Rcpp::Date, std::allocator<Rcpp::Date> > >, Rcpp::Date>' requested here
return range_wrap_dispatch___impl<InputIterator,T>( first, last, typename ::Rcpp::traits::r_type_traits<T>::r_category() ) ;
^
/Library/Frameworks/R.framework/Versions/3.0/Resources/library/Rcpp/include/Rcpp/internal/wrap.h:374:9: note: in instantiation of function template specialization 'Rcpp::internal::range_wrap_dispatch<__gnu_cxx::__normal_iterator<const Rcpp::Date *, std::vector<Rcpp::Date, std::allocator<Rcpp::Date> > >, Rcpp::Date>' requested here
return range_wrap_dispatch<InputIterator,typename traits::remove_reference<typename std::iterator_traits<InputIterator>::value_type>::type >( first, last ) ;
^
/Library/Frameworks/R.framework/Versions/3.0/Resources/library/Rcpp/include/Rcpp/internal/wrap.h:493:9: note: in instantiation of function template specialization 'Rcpp::internal::range_wrap<__gnu_cxx::__normal_iterator<const Rcpp::Date *, std::vector<Rcpp::Date, std::allocator<Rcpp::Date> > > >' requested here
return range_wrap( object.begin(), object.end() ) ;
^
/Library/Frameworks/R.framework/Versions/3.0/Resources/library/Rcpp/include/Rcpp/internal/wrap.h:501:9: note: in instantiation of function template specialization 'Rcpp::internal::wrap_range_sugar_expression<std::vector<Rcpp::Date, std::allocator<Rcpp::Date> > >' requested here
return wrap_range_sugar_expression( object, typename Rcpp::traits::is_sugar_expression<T>::type() ) ;
^
/Library/Frameworks/R.framework/Versions/3.0/Resources/library/Rcpp/include/Rcpp/internal/wrap.h:508:9: note: (skipping 3 contexts in backtrace; use -ftemplate-backtrace-limit=0 to see all)
return wrap_dispatch_unknown_iterable__logical( object,
^
/Library/Frameworks/R.framework/Versions/3.0/Resources/library/Rcpp/include/Rcpp/internal/wrap.h:723:9: note: in instantiation of function template specialization 'Rcpp::internal::wrap_dispatch_unknown<std::vector<Rcpp::Date, std::allocator<Rcpp::Date> > >' requested here
return wrap_dispatch_unknown( object, typename ::Rcpp::traits::is_convertible<T,SEXP>::type() ) ;
^
/Library/Frameworks/R.framework/Versions/3.0/Resources/library/Rcpp/include/Rcpp/internal/wrap.h:740:9: note: in instantiation of function template specialization 'Rcpp::internal::wrap_dispatch_eigen<std::vector<Rcpp::Date, std::allocator<Rcpp::Date> > >' requested here
return wrap_dispatch_eigen( object, typename traits::is_eigen_base<T>::type() ) ;
^
/Library/Frameworks/R.framework/Versions/3.0/Resources/library/Rcpp/include/Rcpp/internal/wrap.h:760:9: note: in instantiation of function template specialization 'Rcpp::internal::wrap_dispatch_unknown_importable<std::vector<Rcpp::Date, std::allocator<Rcpp::Date> > >' requested here
return wrap_dispatch_unknown_importable( object, typename ::Rcpp::traits::is_importer<T>::type() ) ;
^
/Library/Frameworks/R.framework/Versions/3.0/Resources/library/Rcpp/include/Rcpp/internal/wrap.h:863:9: note: in instantiation of function template specialization 'Rcpp::internal::wrap_dispatch<std::vector<Rcpp::Date, std::allocator<Rcpp::Date> > >' requested here
return internal::wrap_dispatch( object, typename ::Rcpp::traits::wrap_type_traits<T>::wrap_category() ) ;
^
/Library/Frameworks/R.framework/Versions/3.0/Resources/library/Rcpp/include/Rcpp/DateVector.h:54:47: note: in instantiation of function template specialization 'Rcpp::wrap<std::vector<Rcpp::Date, std::allocator<Rcpp::Date> > >' requested here
inline operator SEXP() const { return wrap( v ) ; }
^
In file included from disop.cpp:33:
In file included from /Library/Frameworks/R.framework/Versions/3.0/Resources/library/RcppClassic/include/RcppClassic.h:27:
In file included from /Library/Frameworks/R.framework/Versions/3.0/Resources/library/Rcpp/include/RcppCommon.h:117:
/Library/Frameworks/R.framework/Versions/3.0/Resources/library/Rcpp/include/Rcpp/internal/wrap.h:106:43: warning: implicit conversion changes signedness: 'size_t' (aka 'unsigned long') to 'R_xlen_t' (aka 'long') [-Wsign-conversion]
SEXP x = PROTECT( Rf_allocVector( RTYPE, size ) );
˜˜˜˜˜˜˜˜˜˜˜˜˜˜ ^˜˜˜
/Library/Frameworks/R.framework/Resources/include/Rinternals.h:547:31: note: expanded from macro 'PROTECT'
#define PROTECT(s) Rf_protect(s)
^
In file included from disop.cpp:33:
In file included from /Library/Frameworks/R.framework/Versions/3.0/Resources/library/RcppClassic/include/RcppClassic.h:27:
In file included from /Library/Frameworks/R.framework/Versions/3.0/Resources/library/Rcpp/include/RcppCommon.h:117:
/Library/Frameworks/R.framework/Versions/3.0/Resources/library/Rcpp/include/Rcpp/internal/wrap.h:104:16: warning: implicit conversion changes signedness: 'typename iterator_traits<__normal_iterator<const Datetime *, vector<Datetime, allocator<Datetime> > > >::difference_type' (aka 'long') to 'size_t' (aka 'unsigned long') [-Wsign-conversion]
size_t size = std::distance( first, last ) ;
˜˜˜˜ ^˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜
/Library/Frameworks/R.framework/Versions/3.0/Resources/library/Rcpp/include/Rcpp/internal/wrap.h:178:9: note: in instantiation of function template specialization 'Rcpp::internal::primitive_range_wrap__impl<__gnu_cxx::__normal_iterator<const Rcpp::Datetime *, std::vector<Rcpp::Datetime, std::allocator<Rcpp::Datetime> > >, Rcpp::Datetime>' requested here
return primitive_range_wrap__impl<InputIterator,T>( first, last, typename ::Rcpp::traits::r_sexptype_needscast<T>() ) ;
^
/Library/Frameworks/R.framework/Versions/3.0/Resources/library/Rcpp/include/Rcpp/internal/wrap.h:364:9: note: in instantiation of function template specialization 'Rcpp::internal::range_wrap_dispatch___impl<__gnu_cxx::__normal_iterator<const Rcpp::Datetime *, std::vector<Rcpp::Datetime, std::allocator<Rcpp::Datetime> > >, Rcpp::Datetime>' requested here
return range_wrap_dispatch___impl<InputIterator,T>( first, last, typename ::Rcpp::traits::r_type_traits<T>::r_category() ) ;
^
/Library/Frameworks/R.framework/Versions/3.0/Resources/library/Rcpp/include/Rcpp/internal/wrap.h:374:9: note: in instantiation of function template specialization 'Rcpp::internal::range_wrap_dispatch<__gnu_cxx::__normal_iterator<const Rcpp::Datetime *, std::vector<Rcpp::Datetime, std::allocator<Rcpp::Datetime> > >, Rcpp::Datetime>' requested here
return range_wrap_dispatch<InputIterator,typename traits::remove_reference<typename std::iterator_traits<InputIterator>::value_type>::type >( first, last ) ;
^
/Library/Frameworks/R.framework/Versions/3.0/Resources/library/Rcpp/include/Rcpp/internal/wrap.h:493:9: note: in instantiation of function template specialization 'Rcpp::internal::range_wrap<__gnu_cxx::__normal_iterator<const Rcpp::Datetime *, std::vector<Rcpp::Datetime, std::allocator<Rcpp::Datetime> > > >' requested here
return range_wrap( object.begin(), object.end() ) ;
^
/Library/Frameworks/R.framework/Versions/3.0/Resources/library/Rcpp/include/Rcpp/internal/wrap.h:501:9: note: in instantiation of function template specialization 'Rcpp::internal::wrap_range_sugar_expression<std::vector<Rcpp::Datetime, std::allocator<Rcpp::Datetime> > >' requested here
return wrap_range_sugar_expression( object, typename Rcpp::traits::is_sugar_expression<T>::type() ) ;
^
/Library/Frameworks/R.framework/Versions/3.0/Resources/library/Rcpp/include/Rcpp/internal/wrap.h:508:9: note: (skipping 3 contexts in backtrace; use -ftemplate-backtrace-limit=0 to see all)
return wrap_dispatch_unknown_iterable__logical( object,
^
/Library/Frameworks/R.framework/Versions/3.0/Resources/library/Rcpp/include/Rcpp/internal/wrap.h:723:9: note: in instantiation of function template specialization 'Rcpp::internal::wrap_dispatch_unknown<std::vector<Rcpp::Datetime, std::allocator<Rcpp::Datetime> > >' requested here
return wrap_dispatch_unknown( object, typename ::Rcpp::traits::is_convertible<T,SEXP>::type() ) ;
^
/Library/Frameworks/R.framework/Versions/3.0/Resources/library/Rcpp/include/Rcpp/internal/wrap.h:740:9: note: in instantiation of function template specialization 'Rcpp::internal::wrap_dispatch_eigen<std::vector<Rcpp::Datetime, std::allocator<Rcpp::Datetime> > >' requested here
return wrap_dispatch_eigen( object, typename traits::is_eigen_base<T>::type() ) ;
^
/Library/Frameworks/R.framework/Versions/3.0/Resources/library/Rcpp/include/Rcpp/internal/wrap.h:760:9: note: in instantiation of function template specialization 'Rcpp::internal::wrap_dispatch_unknown_importable<std::vector<Rcpp::Datetime, std::allocator<Rcpp::Datetime> > >' requested here
return wrap_dispatch_unknown_importable( object, typename ::Rcpp::traits::is_importer<T>::type() ) ;
^
/Library/Frameworks/R.framework/Versions/3.0/Resources/library/Rcpp/include/Rcpp/internal/wrap.h:863:9: note: in instantiation of function template specialization 'Rcpp::internal::wrap_dispatch<std::vector<Rcpp::Datetime, std::allocator<Rcpp::Datetime> > >' requested here
return internal::wrap_dispatch( object, typename ::Rcpp::traits::wrap_type_traits<T>::wrap_category() ) ;
^
/Library/Frameworks/R.framework/Versions/3.0/Resources/library/Rcpp/include/Rcpp/DatetimeVector.h:54:47: note: in instantiation of function template specialization 'Rcpp::wrap<std::vector<Rcpp::Datetime, std::allocator<Rcpp::Datetime> > >' requested here
inline operator SEXP() const { return wrap( v ) ; }
^
In file included from disop.cpp:33:
In file included from /Library/Frameworks/R.framework/Versions/3.0/Resources/library/RcppClassic/include/RcppClassic.h:27:
In file included from /Library/Frameworks/R.framework/Versions/3.0/Resources/library/Rcpp/include/RcppCommon.h:117:
/Library/Frameworks/R.framework/Versions/3.0/Resources/library/Rcpp/include/Rcpp/internal/wrap.h:106:43: warning: implicit conversion changes signedness: 'size_t' (aka 'unsigned long') to 'R_xlen_t' (aka 'long') [-Wsign-conversion]
SEXP x = PROTECT( Rf_allocVector( RTYPE, size ) );
˜˜˜˜˜˜˜˜˜˜˜˜˜˜ ^˜˜˜
/Library/Frameworks/R.framework/Resources/include/Rinternals.h:547:31: note: expanded from macro 'PROTECT'
#define PROTECT(s) Rf_protect(s)
^
In file included from disop.cpp:33:
In file included from /Library/Frameworks/R.framework/Versions/3.0/Resources/library/RcppClassic/include/RcppClassic.h:29:
In file included from /Library/Frameworks/R.framework/Versions/3.0/Resources/library/Rcpp/include/Rcpp.h:81:
In file included from /Library/Frameworks/R.framework/Versions/3.0/Resources/library/Rcpp/include/Rcpp/api/meat/meat.h:29:
/Library/Frameworks/R.framework/Versions/3.0/Resources/library/Rcpp/include/Rcpp/api/meat/Matrix.h:38:28: warning: implicit conversion changes signedness: 'const int' to 'const size_t' (aka 'const unsigned long') [-Wsign-conversion]
VECTOR( Dimension( nrows_, ncols ) ),
˜˜˜˜˜˜˜˜˜ ^˜˜˜˜˜
/Library/Frameworks/R.framework/Versions/3.0/Resources/library/RcppClassic/include/classic/RcppMatrix__backward.h:34:61: note: in instantiation of member function 'Rcpp::Matrix<13>::Matrix' requested here
Rcpp::Matrix< Rcpp::traits::r_sexptype_traits<T>::rtype > mat( nx, ny ) ;
^
/Library/Frameworks/R.framework/Versions/3.0/Resources/library/RcppClassic/include/classic/RcppMatrix__backward.h:44:9: note: in instantiation of function template specialization 'Rcpp::internal::wrap__old__rcppmatrix<int>' requested here
return internal::wrap__old__rcppmatrix( x );
^
In file included from disop.cpp:33:
In file included from /Library/Frameworks/R.framework/Versions/3.0/Resources/library/RcppClassic/include/RcppClassic.h:29:
In file included from /Library/Frameworks/R.framework/Versions/3.0/Resources/library/Rcpp/include/Rcpp.h:81:
In file included from /Library/Frameworks/R.framework/Versions/3.0/Resources/library/Rcpp/include/Rcpp/api/meat/meat.h:29:
/Library/Frameworks/R.framework/Versions/3.0/Resources/library/Rcpp/include/Rcpp/api/meat/Matrix.h:38:36: warning: implicit conversion changes signedness: 'const int' to 'const size_t' (aka 'const unsigned long') [-Wsign-conversion]
VECTOR( Dimension( nrows_, ncols ) ),
˜˜˜˜˜˜˜˜˜ ^˜˜˜˜
/Library/Frameworks/R.framework/Versions/3.0/Resources/library/Rcpp/include/Rcpp/api/meat/Matrix.h:38:28: warning: implicit conversion changes signedness: 'const int' to 'const size_t' (aka 'const unsigned long') [-Wsign-conversion]
VECTOR( Dimension( nrows_, ncols ) ),
˜˜˜˜˜˜˜˜˜ ^˜˜˜˜˜
/Library/Frameworks/R.framework/Versions/3.0/Resources/library/RcppClassic/include/classic/RcppMatrix__backward.h:34:61: note: in instantiation of member function 'Rcpp::Matrix<14>::Matrix' requested here
Rcpp::Matrix< Rcpp::traits::r_sexptype_traits<T>::rtype > mat( nx, ny ) ;
^
/Library/Frameworks/R.framework/Versions/3.0/Resources/library/RcppClassic/include/classic/RcppMatrix__backward.h:48:9: note: in instantiation of function template specialization 'Rcpp::internal::wrap__old__rcppmatrix<double>' requested here
return internal::wrap__old__rcppmatrix( x );
^
In file included from disop.cpp:33:
In file included from /Library/Frameworks/R.framework/Versions/3.0/Resources/library/RcppClassic/include/RcppClassic.h:29:
In file included from /Library/Frameworks/R.framework/Versions/3.0/Resources/library/Rcpp/include/Rcpp.h:81:
In file included from /Library/Frameworks/R.framework/Versions/3.0/Resources/library/Rcpp/include/Rcpp/api/meat/meat.h:29:
/Library/Frameworks/R.framework/Versions/3.0/Resources/library/Rcpp/include/Rcpp/api/meat/Matrix.h:38:36: warning: implicit conversion changes signedness: 'const int' to 'const size_t' (aka 'const unsigned long') [-Wsign-conversion]
VECTOR( Dimension( nrows_, ncols ) ),
˜˜˜˜˜˜˜˜˜ ^˜˜˜˜
In file included from disop.cpp:33:
In file included from /Library/Frameworks/R.framework/Versions/3.0/Resources/library/RcppClassic/include/RcppClassic.h:28:
In file included from /Library/Frameworks/R.framework/Versions/3.0/Resources/library/RcppClassic/include/classic/classic.h:36:
In file included from /Library/Frameworks/R.framework/Versions/3.0/Resources/library/RcppClassic/include/classic/RcppResultSet.h:39:
/Library/Frameworks/R.framework/Versions/3.0/Resources/library/RcppClassic/include/classic/RcppVector.h:66:23: warning: implicit conversion changes signedness: 'int' to 'size_t' (aka 'unsigned long') [-Wsign-conversion]
v = (T *) R_alloc(len, sizeof(T));
˜˜˜˜˜˜˜ ^˜˜
disop.cpp:172:30: note: in instantiation of member function 'RcppVector<double>::RcppVector' requested here
RcppVector<double> masses = RcppVector<double>(v_masses);
^
In file included from disop.cpp:26:
In file included from ./imslib/src/ims/decomp/realmassdecomposer.h:7:
./imslib/src/ims/decomp/integermassdecomposer.h:494:9: warning: implicit conversion loses integer precision: 'size_type' (aka 'unsigned long') to 'decomposition_value_type' (aka 'unsigned int') [-Wshorten-64-to-32]
return getAllDecompositions(mass).size();
˜˜˜˜˜˜ ^˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜
/usr/include/c++/4.2.1/memory:258:21: note: in instantiation of member function 'ims::IntegerMassDecomposer<unsigned long, unsigned int>::getNumberOfDecompositions' requested here
˜auto_ptr() { delete _M_ptr; }
^
./imslib/src/ims/decomp/realmassdecomposer.h:33:7: note: in instantiation of member function 'std::auto_ptr<ims::IntegerMassDecomposer<unsigned long, unsigned int> >::˜auto_ptr' requested here
class RealMassDecomposer {
^
disop.cpp:637:49: warning: implicit conversion changes signedness: 'size_type' (aka 'unsigned long') to 'R_xlen_t' (aka 'long') [-Wsign-conversion]
SEXP isotopes = PROTECT(Rf_allocVector(VECSXP, scores.size()));
˜˜˜˜˜˜˜˜˜˜˜˜˜˜ ^˜˜˜˜˜˜˜˜˜˜˜˜
/Library/Frameworks/R.framework/Resources/include/Rinternals.h:547:31: note: expanded from macro 'PROTECT'
#define PROTECT(s) Rf_protect(s)
^
disop.cpp:342:9: note: in instantiation of function template specialization 'rlistScores<double>' requested here
rl = rlistScores(scores, Rf_asInteger(z));
^
disop.cpp:649:9: warning: implicit conversion changes signedness: 'unsigned int' to 'int' [-Wsign-conversion]
score(i) = it->first;
˜˜˜˜˜ ^
disop.cpp:651:19: warning: implicit conversion changes signedness: 'unsigned int' to 'int' [-Wsign-conversion]
exactmass(i) = it->second.getMass();
˜˜˜˜˜˜˜˜˜ ^
disop.cpp:652:16: warning: implicit conversion changes signedness: 'unsigned int' to 'int' [-Wsign-conversion]
charge(i) = z;
˜˜˜˜˜˜ ^
disop.cpp:658:7: warning: implicit conversion changes signedness: 'unsigned int' to 'int' [-Wsign-conversion]
DBE(i) = getDBE(it->second, z);
˜˜˜ ^
disop.cpp:669:44: warning: implicit conversion changes signedness: 'int' to 'size_type' (aka 'unsigned long') [-Wsign-conversion]
REAL(tmp_isotopes)[0 + 2*j] = masses[j];
˜˜˜˜˜˜ ^
disop.cpp:670:49: warning: implicit conversion changes signedness: 'int' to 'size_type' (aka 'unsigned long') [-Wsign-conversion]
REAL(tmp_isotopes)[1 + 2*j] = intensities[j];
˜˜˜˜˜˜˜˜˜˜˜ ^
disop.cpp:628:27: warning: implicit conversion loses integer precision: 'size_type' (aka 'unsigned long') to 'int' [-Wshorten-64-to-32]
RcppVector<double> score(scores.size());
˜˜˜˜˜ ^˜˜˜˜˜˜˜˜˜˜˜˜
disop.cpp:629:31: warning: implicit conversion loses integer precision: 'size_type' (aka 'unsigned long') to 'int' [-Wshorten-64-to-32]
RcppVector<double> exactmass(scores.size());
˜˜˜˜˜˜˜˜˜ ^˜˜˜˜˜˜˜˜˜˜˜˜
disop.cpp:630:25: warning: implicit conversion loses integer precision: 'size_type' (aka 'unsigned long') to 'int' [-Wshorten-64-to-32]
RcppVector<int> charge(scores.size());
˜˜˜˜˜˜ ^˜˜˜˜˜˜˜˜˜˜˜˜
disop.cpp:635:25: warning: implicit conversion loses integer precision: 'size_type' (aka 'unsigned long') to 'int' [-Wshorten-64-to-32]
RcppVector<double> DBE(scores.size());
˜˜˜ ^˜˜˜˜˜˜˜˜˜˜˜˜
disop.cpp:665:12: warning: implicit conversion loses integer precision: 'size_type' (aka 'unsigned long') to 'int' [-Wshorten-64-to-32]
int ny = masses.size();
˜˜ ^˜˜˜˜˜˜˜˜˜˜˜˜
In file included from disop.cpp:33:
In file included from /Library/Frameworks/R.framework/Versions/3.0/Resources/library/RcppClassic/include/RcppClassic.h:28:
In file included from /Library/Frameworks/R.framework/Versions/3.0/Resources/library/RcppClassic/include/classic/classic.h:36:
In file included from /Library/Frameworks/R.framework/Versions/3.0/Resources/library/RcppClassic/include/classic/RcppResultSet.h:39:
/Library/Frameworks/R.framework/Versions/3.0/Resources/library/RcppClassic/include/classic/RcppVector.h:80:23: warning: implicit conversion changes signedness: 'int' to 'size_t' (aka 'unsigned long') [-Wsign-conversion]
v = (T *) R_alloc(len, sizeof(T));
˜˜˜˜˜˜˜ ^˜˜
disop.cpp:628:21: note: in instantiation of member function 'RcppVector<double>::RcppVector' requested here
RcppVector<double> score(scores.size());
^
disop.cpp:342:9: note: in instantiation of function template specialization 'rlistScores<double>' requested here
rl = rlistScores(scores, Rf_asInteger(z));
^
In file included from disop.cpp:33:
In file included from /Library/Frameworks/R.framework/Versions/3.0/Resources/library/RcppClassic/include/RcppClassic.h:28:
In file included from /Library/Frameworks/R.framework/Versions/3.0/Resources/library/RcppClassic/include/classic/classic.h:36:
In file included from /Library/Frameworks/R.framework/Versions/3.0/Resources/library/RcppClassic/include/classic/RcppResultSet.h:39:
/Library/Frameworks/R.framework/Versions/3.0/Resources/library/RcppClassic/include/classic/RcppVector.h:80:23: warning: implicit conversion changes signedness: 'int' to 'size_t' (aka 'unsigned long') [-Wsign-conversion]
v = (T *) R_alloc(len, sizeof(T));
˜˜˜˜˜˜˜ ^˜˜
disop.cpp:630:18: note: in instantiation of member function 'RcppVector<int>::RcppVector' requested here
RcppVector<int> charge(scores.size());
^
disop.cpp:342:9: note: in instantiation of function template specialization 'rlistScores<double>' requested here
rl = rlistScores(scores, Rf_asInteger(z));
^
In file included from disop.cpp:33:
In file included from /Library/Frameworks/R.framework/Versions/3.0/Resources/library/RcppClassic/include/RcppClassic.h:27:
In file included from /Library/Frameworks/R.framework/Versions/3.0/Resources/library/Rcpp/include/RcppCommon.h:117:
/Library/Frameworks/R.framework/Versions/3.0/Resources/library/Rcpp/include/Rcpp/internal/wrap.h:208:16: warning: implicit conversion changes signedness: 'typename iterator_traits<__normal_iterator<const basic_string<char> *, vector<basic_string<char>, allocator<basic_string<char> > > > >::difference_type' (aka 'long') to 'size_t' (aka 'unsigned long') [-Wsign-conversion]
size_t size = std::distance( first, last ) ;
˜˜˜˜ ^˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜
/Library/Frameworks/R.framework/Versions/3.0/Resources/library/Rcpp/include/Rcpp/internal/wrap.h:364:9: note: in instantiation of function template specialization 'Rcpp::internal::range_wrap_dispatch___impl<__gnu_cxx::__normal_iterator<const std::basic_string<char> *, std::vector<std::basic_string<char>, std::allocator<std::basic_string<char> > > >, std::basic_string<char> >' requested here
return range_wrap_dispatch___impl<InputIterator,T>( first, last, typename ::Rcpp::traits::r_type_traits<T>::r_category() ) ;
^
/Library/Frameworks/R.framework/Versions/3.0/Resources/library/Rcpp/include/Rcpp/internal/wrap.h:374:9: note: in instantiation of function template specialization 'Rcpp::internal::range_wrap_dispatch<__gnu_cxx::__normal_iterator<const std::basic_string<char> *, std::vector<std::basic_string<char>, std::allocator<std::basic_string<char> > > >, std::basic_string<char> >' requested here
return range_wrap_dispatch<InputIterator,typename traits::remove_reference<typename std::iterator_traits<InputIterator>::value_type>::type >( first, last ) ;
^
/Library/Frameworks/R.framework/Versions/3.0/Resources/library/Rcpp/include/Rcpp/internal/wrap.h:493:9: note: in instantiation of function template specialization 'Rcpp::internal::range_wrap<__gnu_cxx::__normal_iterator<const std::basic_string<char> *, std::vector<std::basic_string<char>, std::allocator<std::basic_string<char> > > > >' requested here
return range_wrap( object.begin(), object.end() ) ;
^
/Library/Frameworks/R.framework/Versions/3.0/Resources/library/Rcpp/include/Rcpp/internal/wrap.h:501:9: note: in instantiation of function template specialization 'Rcpp::internal::wrap_range_sugar_expression<std::vector<std::basic_string<char>, std::allocator<std::basic_string<char> > > >' requested here
return wrap_range_sugar_expression( object, typename Rcpp::traits::is_sugar_expression<T>::type() ) ;
^
/Library/Frameworks/R.framework/Versions/3.0/Resources/library/Rcpp/include/Rcpp/internal/wrap.h:508:9: note: in instantiation of function template specialization 'Rcpp::internal::wrap_dispatch_unknown_iterable__logical<std::vector<std::basic_string<char>, std::allocator<std::basic_string<char> > > >' requested here
return wrap_dispatch_unknown_iterable__logical( object,
^
/Library/Frameworks/R.framework/Versions/3.0/Resources/library/Rcpp/include/Rcpp/internal/wrap.h:614:9: note: (skipping 5 contexts in backtrace; use -ftemplate-backtrace-limit=0 to see all)
return wrap_dispatch_unknown_iterable__matrix_interface( object,
^
/Library/Frameworks/R.framework/Versions/3.0/Resources/library/Rcpp/include/Rcpp/internal/wrap.h:863:9: note: in instantiation of function template specialization 'Rcpp::internal::wrap_dispatch<std::vector<std::basic_string<char>, std::allocator<std::basic_string<char> > > >' requested here
return internal::wrap_dispatch( object, typename ::Rcpp::traits::wrap_type_traits<T>::wrap_category() ) ;
^
/Library/Frameworks/R.framework/Versions/3.0/Resources/library/RcppClassic/include/classic/RcppResultSet__backward.h:27:19: note: in instantiation of function template specialization 'Rcpp::wrap<std::vector<std::basic_string<char>, std::allocator<std::basic_string<char> > > >' requested here
push_back( name, Rcpp::wrap(t) );
^
/Library/Frameworks/R.framework/Versions/3.0/Resources/library/RcppClassic/include/classic/RcppResultSet.h:58:13: note: in instantiation of function template specialization 'RcppResultSet::add__impl<std::vector<std::basic_string<char>, std::allocator<std::basic_string<char> > > >' requested here
return add__impl( name, object ) ;
^
disop.cpp:679:5: note: in instantiation of function template specialization 'RcppResultSet::add<std::vector<std::basic_string<char>, std::allocator<std::basic_string<char> > > >' requested here
rs.add("formula", formula);
^
disop.cpp:342:9: note: in instantiation of function template specialization 'rlistScores<double>' requested here
rl = rlistScores(scores, Rf_asInteger(z));
^
In file included from disop.cpp:33:
In file included from /Library/Frameworks/R.framework/Versions/3.0/Resources/library/RcppClassic/include/RcppClassic.h:27:
In file included from /Library/Frameworks/R.framework/Versions/3.0/Resources/library/Rcpp/include/RcppCommon.h:117:
/Library/Frameworks/R.framework/Versions/3.0/Resources/library/Rcpp/include/Rcpp/internal/wrap.h:209:44: warning: implicit conversion changes signedness: 'size_t' (aka 'unsigned long') to 'R_xlen_t' (aka 'long') [-Wsign-conversion]
SEXP x = PROTECT( Rf_allocVector( STRSXP, size ) ) ;
˜˜˜˜˜˜˜˜˜˜˜˜˜˜ ^˜˜˜
/Library/Frameworks/R.framework/Resources/include/Rinternals.h:547:31: note: expanded from macro 'PROTECT'
#define PROTECT(s) Rf_protect(s)
^
In file included from disop.cpp:33:
In file included from /Library/Frameworks/R.framework/Versions/3.0/Resources/library/RcppClassic/include/RcppClassic.h:27:
In file included from /Library/Frameworks/R.framework/Versions/3.0/Resources/library/Rcpp/include/RcppCommon.h:117:
/Library/Frameworks/R.framework/Versions/3.0/Resources/library/Rcpp/include/Rcpp/internal/wrap.h:212:22: warning: implicit conversion changes signedness: 'size_t' (aka 'unsigned long') to 'R_xlen_t' (aka 'long') [-Wsign-conversion]
SET_STRING_ELT( x, i, make_charsexp(*first) ) ;
˜˜˜˜˜˜˜˜˜˜˜˜˜˜ ^
/Library/Frameworks/R.framework/Versions/3.0/Resources/library/Rcpp/include/Rcpp/internal/wrap.h:116:16: warning: implicit conversion changes signedness: 'typename iterator_traits<const double *>::difference_type' (aka 'long') to 'size_t' (aka 'unsigned long') [-Wsign-conversion]
size_t size = std::distance( first, last ) ;
˜˜˜˜ ^˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜
/Library/Frameworks/R.framework/Versions/3.0/Resources/library/Rcpp/include/Rcpp/internal/wrap.h:166:9: note: in instantiation of function template specialization 'Rcpp::internal::primitive_range_wrap__impl__nocast<const double *, double>' requested here
return primitive_range_wrap__impl__nocast<InputIterator,T>( first, last, typename std::iterator_traits<InputIterator>::iterator_category() ) ;
^
/Library/Frameworks/R.framework/Versions/3.0/Resources/library/Rcpp/include/Rcpp/internal/wrap.h:178:9: note: in instantiation of function template specialization 'Rcpp::internal::primitive_range_wrap__impl<const double *, double>' requested here
return primitive_range_wrap__impl<InputIterator,T>( first, last, typename ::Rcpp::traits::r_sexptype_needscast<T>() ) ;
^
/Library/Frameworks/R.framework/Versions/3.0/Resources/library/Rcpp/include/Rcpp/internal/wrap.h:364:9: note: in instantiation of function template specialization 'Rcpp::internal::range_wrap_dispatch___impl<const double *, double>' requested here
return range_wrap_dispatch___impl<InputIterator,T>( first, last, typename ::Rcpp::traits::r_type_traits<T>::r_category() ) ;
^
/Library/Frameworks/R.framework/Versions/3.0/Resources/library/Rcpp/include/Rcpp/internal/wrap.h:374:9: note: in instantiation of function template specialization 'Rcpp::internal::range_wrap_dispatch<const double *, double>' requested here
return range_wrap_dispatch<InputIterator,typename traits::remove_reference<typename std::iterator_traits<InputIterator>::value_type>::type >( first, last ) ;
^
/Library/Frameworks/R.framework/Versions/3.0/Resources/library/Rcpp/include/Rcpp/internal/wrap.h:493:9: note: in instantiation of function template specialization 'Rcpp::internal::range_wrap<const double *>' requested here
return range_wrap( object.begin(), object.end() ) ;
^
/Library/Frameworks/R.framework/Versions/3.0/Resources/library/Rcpp/include/Rcpp/internal/wrap.h:501:9: note: (skipping 7 contexts in backtrace; use -ftemplate-backtrace-limit=0 to see all)
return wrap_range_sugar_expression( object, typename Rcpp::traits::is_sugar_expression<T>::type() ) ;
^
/Library/Frameworks/R.framework/Versions/3.0/Resources/library/Rcpp/include/Rcpp/internal/wrap.h:863:9: note: in instantiation of function template specialization 'Rcpp::internal::wrap_dispatch<RcppVector<double> >' requested here
return internal::wrap_dispatch( object, typename ::Rcpp::traits::wrap_type_traits<T>::wrap_category() ) ;
^
/Library/Frameworks/R.framework/Versions/3.0/Resources/library/RcppClassic/include/classic/RcppResultSet__backward.h:27:19: note: in instantiation of function template specialization 'Rcpp::wrap<RcppVector<double> >' requested here
push_back( name, Rcpp::wrap(t) );
^
/Library/Frameworks/R.framework/Versions/3.0/Resources/library/RcppClassic/include/classic/RcppResultSet.h:58:13: note: in instantiation of function template specialization 'RcppResultSet::add__impl<RcppVector<double> >' requested here
return add__impl( name, object ) ;
^
disop.cpp:680:5: note: in instantiation of function template specialization 'RcppResultSet::add<RcppVector<double> >' requested here
rs.add("score", score);
^
disop.cpp:342:9: note: in instantiation of function template specialization 'rlistScores<double>' requested here
rl = rlistScores(scores, Rf_asInteger(z));
^
In file included from disop.cpp:33:
In file included from /Library/Frameworks/R.framework/Versions/3.0/Resources/library/RcppClassic/include/RcppClassic.h:27:
In file included from /Library/Frameworks/R.framework/Versions/3.0/Resources/library/Rcpp/include/RcppCommon.h:117:
/Library/Frameworks/R.framework/Versions/3.0/Resources/library/Rcpp/include/Rcpp/internal/wrap.h:118:43: warning: implicit conversion changes signedness: 'size_t' (aka 'unsigned long') to 'R_xlen_t' (aka 'long') [-Wsign-conversion]
SEXP x = PROTECT( Rf_allocVector( RTYPE, size ) );
˜˜˜˜˜˜˜˜˜˜˜˜˜˜ ^˜˜˜
/Library/Frameworks/R.framework/Resources/include/Rinternals.h:547:31: note: expanded from macro 'PROTECT'
#define PROTECT(s) Rf_protect(s)
^
In file included from disop.cpp:33:
In file included from /Library/Frameworks/R.framework/Versions/3.0/Resources/library/RcppClassic/include/RcppClassic.h:27:
In file included from /Library/Frameworks/R.framework/Versions/3.0/Resources/library/Rcpp/include/RcppCommon.h:117:
/Library/Frameworks/R.framework/Versions/3.0/Resources/library/Rcpp/include/Rcpp/internal/wrap.h:130:17: warning: implicit conversion changes signedness: 'int' to 'unsigned long' [-Wsign-conversion]
switch (size - i){
˜ ^
/Library/Frameworks/R.framework/Versions/3.0/Resources/library/Rcpp/include/Rcpp/internal/wrap.h:121:26: warning: implicit conversion loses integer precision: 'size_t' (aka 'unsigned long') to 'int' [-Wshorten-64-to-32]
int __trip_count = size >> 2 ;
˜˜˜˜˜˜˜˜˜˜˜˜ ˜˜˜˜˜^˜˜˜
88 warnings generated.
clang++ -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -I/usr/local/include -I"/Library/Frameworks/R.framework/Versions/3.0/Resources/library/RcppClassic/include" -I"/Library/Frameworks/R.framework/Versions/3.0/Resources/library/Rcpp/include" -I./imslib/src/ -fPIC -mtune=native -g -O2 -Wall -pedantic -Wconversion -c imslib/src/ims/element.cpp -o imslib/src/ims/element.o
In file included from imslib/src/ims/element.cpp:6:
./imslib/src/ims/element.h:169:35: warning: implicit conversion changes signedness: 'int' to 'size_type' (aka 'unsigned long') [-Wsign-conversion]
if (isotopes.getAbundance(i) > 0.5) {
˜˜˜˜˜˜˜˜ ^
./imslib/src/ims/element.h:175:28: warning: implicit conversion changes signedness: 'int' to 'size_type' (aka 'unsigned long') [-Wsign-conversion]
return isotopes.getMass(i);
˜˜˜˜˜˜˜˜ ^
./imslib/src/ims/element.h:177:35: warning: implicit conversion changes signedness: 'int' to 'size_type' (aka 'unsigned long') [-Wsign-conversion]
if (isotopes.getAbundance(i) > maxval) {
˜˜˜˜˜˜˜˜ ^
./imslib/src/ims/element.h:178:35: warning: implicit conversion changes signedness: 'int' to 'size_type' (aka 'unsigned long') [-Wsign-conversion]
maxval = isotopes.getAbundance(i);
˜˜˜˜˜˜˜˜ ^
./imslib/src/ims/element.h:183:31: warning: implicit conversion changes signedness: 'int' to 'size_type' (aka 'unsigned long') [-Wsign-conversion]
return isotopes.getMass(maxindex);
˜˜˜˜˜˜˜˜ ^˜˜˜˜˜˜˜
5 warnings generated.
clang++ -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -I/usr/local/include -I"/Library/Frameworks/R.framework/Versions/3.0/Resources/library/RcppClassic/include" -I"/Library/Frameworks/R.framework/Versions/3.0/Resources/library/Rcpp/include" -I./imslib/src/ -fPIC -mtune=native -g -O2 -Wall -pedantic -Wconversion -c imslib/src/ims/composedelement.cpp -o imslib/src/ims/composedelement.o
In file included from imslib/src/ims/composedelement.cpp:8:
In file included from ./imslib/src/ims/composedelement.h:7:
./imslib/src/ims/element.h:169:35: warning: implicit conversion changes signedness: 'int' to 'size_type' (aka 'unsigned long') [-Wsign-conversion]
if (isotopes.getAbundance(i) > 0.5) {
˜˜˜˜˜˜˜˜ ^
./imslib/src/ims/element.h:175:28: warning: implicit conversion changes signedness: 'int' to 'size_type' (aka 'unsigned long') [-Wsign-conversion]
return isotopes.getMass(i);
˜˜˜˜˜˜˜˜ ^
./imslib/src/ims/element.h:177:35: warning: implicit conversion changes signedness: 'int' to 'size_type' (aka 'unsigned long') [-Wsign-conversion]
if (isotopes.getAbundance(i) > maxval) {
˜˜˜˜˜˜˜˜ ^
./imslib/src/ims/element.h:178:35: warning: implicit conversion changes signedness: 'int' to 'size_type' (aka 'unsigned long') [-Wsign-conversion]
maxval = isotopes.getAbundance(i);
˜˜˜˜˜˜˜˜ ^
./imslib/src/ims/element.h:183:31: warning: implicit conversion changes signedness: 'int' to 'size_type' (aka 'unsigned long') [-Wsign-conversion]
return isotopes.getMass(maxindex);
˜˜˜˜˜˜˜˜ ^˜˜˜˜˜˜˜
5 warnings generated.
clang++ -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -I/usr/local/include -I"/Library/Frameworks/R.framework/Versions/3.0/Resources/library/RcppClassic/include" -I"/Library/Frameworks/R.framework/Versions/3.0/Resources/library/Rcpp/include" -I./imslib/src/ -fPIC -mtune=native -g -O2 -Wall -pedantic -Wconversion -c imslib/src/ims/isotopedistribution.cpp -o imslib/src/ims/isotopedistribution.o
clang++ -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -I/usr/local/include -I"/Library/Frameworks/R.framework/Versions/3.0/Resources/library/RcppClassic/include" -I"/Library/Frameworks/R.framework/Versions/3.0/Resources/library/Rcpp/include" -I./imslib/src/ -fPIC -mtune=native -g -O2 -Wall -pedantic -Wconversion -c imslib/src/ims/alphabet.cpp -o imslib/src/ims/alphabet.o
In file included from imslib/src/ims/alphabet.cpp:6:
In file included from ./imslib/src/ims/alphabet.h:8:
./imslib/src/ims/element.h:169:35: warning: implicit conversion changes signedness: 'int' to 'size_type' (aka 'unsigned long') [-Wsign-conversion]
if (isotopes.getAbundance(i) > 0.5) {
˜˜˜˜˜˜˜˜ ^
./imslib/src/ims/element.h:175:28: warning: implicit conversion changes signedness: 'int' to 'size_type' (aka 'unsigned long') [-Wsign-conversion]
return isotopes.getMass(i);
˜˜˜˜˜˜˜˜ ^
./imslib/src/ims/element.h:177:35: warning: implicit conversion changes signedness: 'int' to 'size_type' (aka 'unsigned long') [-Wsign-conversion]
if (isotopes.getAbundance(i) > maxval) {
˜˜˜˜˜˜˜˜ ^
./imslib/src/ims/element.h:178:35: warning: implicit conversion changes signedness: 'int' to 'size_type' (aka 'unsigned long') [-Wsign-conversion]
maxval = isotopes.getAbundance(i);
˜˜˜˜˜˜˜˜ ^
./imslib/src/ims/element.h:183:31: warning: implicit conversion changes signedness: 'int' to 'size_type' (aka 'unsigned long') [-Wsign-conversion]
return isotopes.getMass(maxindex);
˜˜˜˜˜˜˜˜ ^˜˜˜˜˜˜˜
5 warnings generated.
clang++ -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -I/usr/local/include -I"/Library/Frameworks/R.framework/Versions/3.0/Resources/library/RcppClassic/include" -I"/Library/Frameworks/R.framework/Versions/3.0/Resources/library/Rcpp/include" -I./imslib/src/ -fPIC -mtune=native -g -O2 -Wall -pedantic -Wconversion -c imslib/src/ims/weights.cpp -o imslib/src/ims/weights.o
clang++ -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -I/usr/local/include -I"/Library/Frameworks/R.framework/Versions/3.0/Resources/library/RcppClassic/include" -I"/Library/Frameworks/R.framework/Versions/3.0/Resources/library/Rcpp/include" -I./imslib/src/ -fPIC -mtune=native -g -O2 -Wall -pedantic -Wconversion -c imslib/src/ims/distributedalphabet.cpp -o imslib/src/ims/distributedalphabet.o
In file included from imslib/src/ims/distributedalphabet.cpp:7:
In file included from ./imslib/src/ims/distributedalphabet.h:7:
In file included from ./imslib/src/ims/alphabet.h:8:
./imslib/src/ims/element.h:169:35: warning: implicit conversion changes signedness: 'int' to 'size_type' (aka 'unsigned long') [-Wsign-conversion]
if (isotopes.getAbundance(i) > 0.5) {
˜˜˜˜˜˜˜˜ ^
./imslib/src/ims/element.h:175:28: warning: implicit conversion changes signedness: 'int' to 'size_type' (aka 'unsigned long') [-Wsign-conversion]
return isotopes.getMass(i);
˜˜˜˜˜˜˜˜ ^
./imslib/src/ims/element.h:177:35: warning: implicit conversion changes signedness: 'int' to 'size_type' (aka 'unsigned long') [-Wsign-conversion]
if (isotopes.getAbundance(i) > maxval) {
˜˜˜˜˜˜˜˜ ^
./imslib/src/ims/element.h:178:35: warning: implicit conversion changes signedness: 'int' to 'size_type' (aka 'unsigned long') [-Wsign-conversion]
maxval = isotopes.getAbundance(i);
˜˜˜˜˜˜˜˜ ^
./imslib/src/ims/element.h:183:31: warning: implicit conversion changes signedness: 'int' to 'size_type' (aka 'unsigned long') [-Wsign-conversion]
return isotopes.getMass(maxindex);
˜˜˜˜˜˜˜˜ ^˜˜˜˜˜˜˜
5 warnings generated.
clang++ -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -I/usr/local/include -I"/Library/Frameworks/R.framework/Versions/3.0/Resources/library/RcppClassic/include" -I"/Library/Frameworks/R.framework/Versions/3.0/Resources/library/Rcpp/include" -I./imslib/src/ -fPIC -mtune=native -g -O2 -Wall -pedantic -Wconversion -c imslib/src/ims/transformation.cpp -o imslib/src/ims/transformation.o
clang++ -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -I/usr/local/include -I"/Library/Frameworks/R.framework/Versions/3.0/Resources/library/RcppClassic/include" -I"/Library/Frameworks/R.framework/Versions/3.0/Resources/library/Rcpp/include" -I./imslib/src/ -fPIC -mtune=native -g -O2 -Wall -pedantic -Wconversion -c imslib/src/ims/isotopespecies.cpp -o imslib/src/ims/isotopespecies.o
imslib/src/ims/isotopespecies.cpp:85:37: warning: implicit conversion changes signedness: 'unsigned int' to 'int' [-Wsign-conversion]
updateCoefficients(1, indexes, 0, power, power, temp_container);
˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜ ^˜˜˜˜
imslib/src/ims/isotopespecies.cpp:85:44: warning: implicit conversion changes signedness: 'unsigned int' to 'int' [-Wsign-conversion]
updateCoefficients(1, indexes, 0, power, power, temp_container);
˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜ ^˜˜˜˜
imslib/src/ims/isotopespecies.cpp:125:37: warning: implicit conversion changes signedness: 'int' to 'size_type' (aka 'unsigned long') [-Wsign-conversion]
} else if (coefficient >= indexes[i]+1) {
˜˜˜˜˜˜˜ ^
imslib/src/ims/isotopespecies.cpp:126:17: warning: implicit conversion changes signedness: 'int' to 'size_type' (aka 'unsigned long') [-Wsign-conversion]
updateIndexes(i, indexes);
˜˜˜˜˜˜˜˜˜˜˜˜˜ ^
imslib/src/ims/isotopespecies.cpp:129:44: warning: implicit conversion changes signedness: 'int' to 'size_type' (aka 'unsigned long') [-Wsign-conversion]
size_type mass = (coefficient >= indexes[i]+1) ? (indexes[i]+1): 1;
˜˜˜˜˜˜˜ ^
imslib/src/ims/isotopespecies.cpp:129:61: warning: implicit conversion changes signedness: 'int' to 'size_type' (aka 'unsigned long') [-Wsign-conversion]
size_type mass = (coefficient >= indexes[i]+1) ? (indexes[i]+1): 1;
˜˜˜˜˜˜˜ ^
imslib/src/ims/isotopespecies.cpp:129:63: warning: operand of ? changes signedness: 'int' to 'size_type' (aka 'unsigned long') [-Wsign-conversion]
size_type mass = (coefficient >= indexes[i]+1) ? (indexes[i]+1): 1;
˜˜˜˜ ˜˜˜˜˜˜˜˜˜˜^˜
imslib/src/ims/isotopespecies.cpp:130:32: warning: implicit conversion changes signedness: 'int' to 'size_type' (aka 'unsigned long') [-Wsign-conversion]
for (size_type j = indexes[i]+2; static_cast<int>(j) <= coefficient; ++j) {
˜ ˜˜˜˜˜˜˜˜˜˜^˜
imslib/src/ims/isotopespecies.cpp:130:30: warning: implicit conversion changes signedness: 'int' to 'size_type' (aka 'unsigned long') [-Wsign-conversion]
for (size_type j = indexes[i]+2; static_cast<int>(j) <= coefficient; ++j) {
˜˜˜˜˜˜˜ ^
imslib/src/ims/isotopespecies.cpp:132:17: warning: implicit conversion changes signedness: 'int' to 'unsigned long' [-Wsign-conversion]
mass /= (j - indexes[i]);
˜ ^˜˜˜˜˜˜˜˜˜
imslib/src/ims/isotopespecies.cpp:132:25: warning: implicit conversion changes signedness: 'int' to 'size_type' (aka 'unsigned long') [-Wsign-conversion]
mass /= (j - indexes[i]);
˜˜˜˜˜˜˜ ^
imslib/src/ims/isotopespecies.cpp:136:27: warning: implicit conversion changes signedness: 'int' to 'size_type' (aka 'unsigned long') [-Wsign-conversion]
(coefficient - indexes[i]) * isotopes[0].mass + indexes[i] * isotopes[i+1].mass,
˜˜˜˜˜˜˜ ^
imslib/src/ims/isotopespecies.cpp:136:60: warning: implicit conversion changes signedness: 'int' to 'size_type' (aka 'unsigned long') [-Wsign-conversion]
(coefficient - indexes[i]) * isotopes[0].mass + indexes[i] * isotopes[i+1].mass,
˜˜˜˜˜˜˜ ^
imslib/src/ims/isotopespecies.cpp:136:75: warning: implicit conversion changes signedness: 'int' to 'size_type' (aka 'unsigned long') [-Wsign-conversion]
(coefficient - indexes[i]) * isotopes[0].mass + indexes[i] * isotopes[i+1].mass,
˜˜˜˜˜˜˜˜ ˜^˜
imslib/src/ims/isotopespecies.cpp:137:81: warning: implicit conversion changes signedness: 'int' to 'size_type' (aka 'unsigned long') [-Wsign-conversion]
mass * std::pow(isotopes[0].abundance, static_cast<int>(coefficient-indexes[i])) *
˜˜˜˜˜˜˜ ^
imslib/src/ims/isotopespecies.cpp:138:26: warning: implicit conversion changes signedness: 'int' to 'size_type' (aka 'unsigned long') [-Wsign-conversion]
std::pow(isotopes[i+1].abundance, static_cast<int>(indexes[i])));
˜˜˜˜˜˜˜˜ ˜^˜
imslib/src/ims/isotopespecies.cpp:138:66: warning: implicit conversion changes signedness: 'int' to 'size_type' (aka 'unsigned long') [-Wsign-conversion]
std::pow(isotopes[i+1].abundance, static_cast<int>(indexes[i])));
˜˜˜˜˜˜˜ ^
imslib/src/ims/isotopespecies.cpp:141:63: warning: implicit conversion changes signedness: 'int' to 'size_type' (aka 'unsigned long') [-Wsign-conversion]
updateCoefficients(i, indexes, counter, coefficient-indexes[i], coefficient, temp_container);
˜˜˜˜˜˜˜ ^
imslib/src/ims/isotopespecies.cpp:145:18: warning: implicit conversion changes signedness: 'int' to 'size_type' (aka 'unsigned long') [-Wsign-conversion]
updateIndexes(i+1, indexes);
˜˜˜˜˜˜˜˜˜˜˜˜˜ ˜^˜
imslib/src/ims/isotopespecies.cpp:149:49: warning: implicit conversion changes signedness: 'int' to 'size_type' (aka 'unsigned long') [-Wsign-conversion]
(coefficient-1)*isotopes[0].mass + isotopes[i+2].mass,
˜˜˜˜˜˜˜˜ ˜^˜
imslib/src/ims/isotopespecies.cpp:150:95: warning: implicit conversion changes signedness: 'int' to 'size_type' (aka 'unsigned long') [-Wsign-conversion]
coefficient * std::pow(isotopes[0].abundance, static_cast<int>(coefficient)-1) * isotopes[i+2].abundance);
˜˜˜˜˜˜˜˜ ˜^˜
21 warnings generated.
clang++ -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -I/usr/local/include -I"/Library/Frameworks/R.framework/Versions/3.0/Resources/library/RcppClassic/include" -I"/Library/Frameworks/R.framework/Versions/3.0/Resources/library/Rcpp/include" -I./imslib/src/ -fPIC -mtune=native -g -O2 -Wall -pedantic -Wconversion -c imslib/src/ims/base/parser/alphabettextparser.cpp -o imslib/src/ims/base/parser/alphabettextparser.o
clang++ -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -I/usr/local/include -I"/Library/Frameworks/R.framework/Versions/3.0/Resources/library/RcppClassic/include" -I"/Library/Frameworks/R.framework/Versions/3.0/Resources/library/Rcpp/include" -I./imslib/src/ -fPIC -mtune=native -g -O2 -Wall -pedantic -Wconversion -c imslib/src/ims/base/parser/distributedalphabettextparser.cpp -o imslib/src/ims/base/parser/distributedalphabettextparser.o
clang++ -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -I/usr/local/include -I"/Library/Frameworks/R.framework/Versions/3.0/Resources/library/RcppClassic/include" -I"/Library/Frameworks/R.framework/Versions/3.0/Resources/library/Rcpp/include" -I./imslib/src/ -fPIC -mtune=native -g -O2 -Wall -pedantic -Wconversion -c imslib/src/ims/base/parser/massestextparser.cpp -o imslib/src/ims/base/parser/massestextparser.o
clang++ -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -I/usr/local/include -I"/Library/Frameworks/R.framework/Versions/3.0/Resources/library/RcppClassic/include" -I"/Library/Frameworks/R.framework/Versions/3.0/Resources/library/Rcpp/include" -I./imslib/src/ -fPIC -mtune=native -g -O2 -Wall -pedantic -Wconversion -c imslib/src/ims/base/parser/moleculesequenceparser.cpp -o imslib/src/ims/base/parser/moleculesequenceparser.o
clang++ -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -I/usr/local/include -I"/Library/Frameworks/R.framework/Versions/3.0/Resources/library/RcppClassic/include" -I"/Library/Frameworks/R.framework/Versions/3.0/Resources/library/Rcpp/include" -I./imslib/src/ -fPIC -mtune=native -g -O2 -Wall -pedantic -Wconversion -c imslib/src/ims/base/parser/standardmoleculesequenceparser.cpp -o imslib/src/ims/base/parser/standardmoleculesequenceparser.o
clang++ -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -I/usr/local/include -I"/Library/Frameworks/R.framework/Versions/3.0/Resources/library/RcppClassic/include" -I"/Library/Frameworks/R.framework/Versions/3.0/Resources/library/Rcpp/include" -I./imslib/src/ -fPIC -mtune=native -g -O2 -Wall -pedantic -Wconversion -c imslib/src/ims/base/parser/keggligandcompoundsparser.cpp -o imslib/src/ims/base/parser/keggligandcompoundsparser.o
imslib/src/ims/base/parser/keggligandcompoundsparser.cpp:53:31: warning: '&&' within '||' [-Wlogical-op-parentheses]
for (; letter_pos < last_pos &&
˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜^˜
imslib/src/ims/base/parser/keggligandcompoundsparser.cpp:53:31: note: place parentheses around the '&&' expression to silence this warning
for (; letter_pos < last_pos &&
^
1 warning generated.
clang++ -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -I/usr/local/include -I"/Library/Frameworks/R.framework/Versions/3.0/Resources/library/RcppClassic/include" -I"/Library/Frameworks/R.framework/Versions/3.0/Resources/library/Rcpp/include" -I./imslib/src/ -fPIC -mtune=native -g -O2 -Wall -pedantic -Wconversion -c imslib/src/ims/base/parser/moleculeionchargemodificationparser.cpp -o imslib/src/ims/base/parser/moleculeionchargemodificationparser.o
clang++ -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -I/usr/local/include -I"/Library/Frameworks/R.framework/Versions/3.0/Resources/library/RcppClassic/include" -I"/Library/Frameworks/R.framework/Versions/3.0/Resources/library/Rcpp/include" -I./imslib/src/ -fPIC -mtune=native -g -O2 -Wall -pedantic -Wconversion -c imslib/src/ims/calib/linepairstabber.cpp -o imslib/src/ims/calib/linepairstabber.o
clang++ -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -I/usr/local/include -I"/Library/Frameworks/R.framework/Versions/3.0/Resources/library/RcppClassic/include" -I"/Library/Frameworks/R.framework/Versions/3.0/Resources/library/Rcpp/include" -I./imslib/src/ -fPIC -mtune=native -g -O2 -Wall -pedantic -Wconversion -c imslib/src/ims/calib/matchmatrix.cpp -o imslib/src/ims/calib/matchmatrix.o
imslib/src/ims/calib/matchmatrix.cpp:34:21: warning: implicit conversion loses integer precision: 'size_t' (aka 'unsigned long') to 'int' [-Wshorten-64-to-32]
matrix[row].start=column;
˜^˜˜˜˜˜
imslib/src/ims/calib/matchmatrix.cpp:35:19: warning: implicit conversion loses integer precision: 'size_t' (aka 'unsigned long') to 'int' [-Wshorten-64-to-32]
matrix[row].end=column;
˜^˜˜˜˜˜
imslib/src/ims/calib/matchmatrix.cpp:94:9: warning: implicit conversion loses integer precision: 'size_t' (aka 'unsigned long') to 'const key_type' (aka 'const int') [-Wshorten-64-to-32]
(*m)[row]=candidate;
˜ ^˜˜
imslib/src/ims/calib/matchmatrix.cpp:121:9: warning: implicit conversion loses integer precision: 'size_t' (aka 'unsigned long') to 'const key_type' (aka 'const int') [-Wshorten-64-to-32]
(*m)[row]=candidate;
˜ ^˜˜
4 warnings generated.
clang++ -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -I/usr/local/include -I"/Library/Frameworks/R.framework/Versions/3.0/Resources/library/RcppClassic/include" -I"/Library/Frameworks/R.framework/Versions/3.0/Resources/library/Rcpp/include" -I./imslib/src/ -fPIC -mtune=native -g -O2 -Wall -pedantic -Wconversion -c imslib/src/ims/calib/linearpointsetmatcher.cpp -o imslib/src/ims/calib/linearpointsetmatcher.o
In file included from imslib/src/ims/calib/linearpointsetmatcher.cpp:11:
./imslib/src/ims/calib/linearpointsetmatcher.h:246:27: warning: implicit conversion changes signedness: 'int' to 'std::size_t' (aka 'unsigned long') [-Wsign-conversion]
MatchMatrix match_matrix(m);
˜˜˜˜˜˜˜˜˜˜˜˜ ^
./imslib/src/ims/calib/linearpointsetmatcher.h:256:21: warning: implicit conversion changes signedness: 'int' to 'std::size_t' (aka 'unsigned long') [-Wsign-conversion]
match_matrix.set(i,l);
˜˜˜˜˜˜˜˜˜˜˜˜ ^
./imslib/src/ims/calib/linearpointsetmatcher.h:256:23: warning: implicit conversion changes signedness: 'int' to 'std::size_t' (aka 'unsigned long') [-Wsign-conversion]
match_matrix.set(i,l);
˜˜˜˜˜˜˜˜˜˜˜˜ ^
./imslib/src/ims/calib/linearpointsetmatcher.h:259:22: warning: implicit conversion changes signedness: 'int' to 'std::size_t' (aka 'unsigned long') [-Wsign-conversion]
match_matrix.set(i,l);
˜˜˜˜˜˜˜˜˜˜˜˜ ^
./imslib/src/ims/calib/linearpointsetmatcher.h:259:24: warning: implicit conversion changes signedness: 'int' to 'std::size_t' (aka 'unsigned long') [-Wsign-conversion]
match_matrix.set(i,l);
˜˜˜˜˜˜˜˜˜˜˜˜ ^
./imslib/src/ims/calib/linearpointsetmatcher.h:269:26: warning: implicit conversion changes signedness: 'const int' to 'std::size_t' (aka 'unsigned long') [-Wsign-conversion]
match_matrix.unset(p->k,p->l);
˜˜˜˜˜˜˜˜˜˜˜˜ ˜˜˜^
./imslib/src/ims/calib/linearpointsetmatcher.h:269:31: warning: implicit conversion changes signedness: 'const int' to 'std::size_t' (aka 'unsigned long') [-Wsign-conversion]
match_matrix.unset(p->k,p->l);
˜˜˜˜˜˜˜˜˜˜˜˜ ˜˜˜^
./imslib/src/ims/calib/linearpointsetmatcher.h:275:24: warning: implicit conversion changes signedness: 'const int' to 'std::size_t' (aka 'unsigned long') [-Wsign-conversion]
match_matrix.set(p->k,p->l);
˜˜˜˜˜˜˜˜˜˜˜˜ ˜˜˜^
./imslib/src/ims/calib/linearpointsetmatcher.h:275:29: warning: implicit conversion changes signedness: 'const int' to 'std::size_t' (aka 'unsigned long') [-Wsign-conversion]
match_matrix.set(p->k,p->l);
˜˜˜˜˜˜˜˜˜˜˜˜ ˜˜˜^
imslib/src/ims/calib/linearpointsetmatcher.cpp:20:2: warning: extra ';' outside of a function is a C++11 extension [-Wc++11-extra-semi]
};
^
10 warnings generated.
clang++ -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -I/usr/local/include -I"/Library/Frameworks/R.framework/Versions/3.0/Resources/library/RcppClassic/include" -I"/Library/Frameworks/R.framework/Versions/3.0/Resources/library/Rcpp/include" -I./imslib/src/ -fPIC -mtune=native -g -O2 -Wall -pedantic -Wconversion -c imslib/src/ims/decomp/realmassdecomposer.cpp -o imslib/src/ims/decomp/realmassdecomposer.o
In file included from imslib/src/ims/decomp/realmassdecomposer.cpp:8:
./imslib/src/ims/decomp/realmassdecomposer.h:55:20: warning: 'long long' is a C++11 extension [-Wc++11-long-long]
typedef unsigned long long number_of_decompositions_type;
^
In file included from imslib/src/ims/decomp/realmassdecomposer.cpp:9:
In file included from ./imslib/src/ims/decomp/decomputils.h:12:
In file included from ./imslib/src/ims/alphabet.h:8:
./imslib/src/ims/element.h:169:35: warning: implicit conversion changes signedness: 'int' to 'size_type' (aka 'unsigned long') [-Wsign-conversion]
if (isotopes.getAbundance(i) > 0.5) {
˜˜˜˜˜˜˜˜ ^
./imslib/src/ims/element.h:175:28: warning: implicit conversion changes signedness: 'int' to 'size_type' (aka 'unsigned long') [-Wsign-conversion]
return isotopes.getMass(i);
˜˜˜˜˜˜˜˜ ^
./imslib/src/ims/element.h:177:35: warning: implicit conversion changes signedness: 'int' to 'size_type' (aka 'unsigned long') [-Wsign-conversion]
if (isotopes.getAbundance(i) > maxval) {
˜˜˜˜˜˜˜˜ ^
./imslib/src/ims/element.h:178:35: warning: implicit conversion changes signedness: 'int' to 'size_type' (aka 'unsigned long') [-Wsign-conversion]
maxval = isotopes.getAbundance(i);
˜˜˜˜˜˜˜˜ ^
./imslib/src/ims/element.h:183:31: warning: implicit conversion changes signedness: 'int' to 'size_type' (aka 'unsigned long') [-Wsign-conversion]
return isotopes.getMass(maxindex);
˜˜˜˜˜˜˜˜ ^˜˜˜˜˜˜˜
In file included from imslib/src/ims/decomp/realmassdecomposer.cpp:8:
In file included from ./imslib/src/ims/decomp/realmassdecomposer.h:7:
./imslib/src/ims/decomp/integermassdecomposer.h:222:72: warning: implicit conversion changes signedness: 'size_type' (aka 'unsigned long') to 'const difference_type' (aka 'const long') [-Wsign-conversion]
typename residues_table_row_type::iterator it = _ertable[1].begin() + it_inc;
˜˜˜˜˜˜˜˜ ^˜˜˜˜˜
./imslib/src/ims/decomp/integermassdecomposer.h:192:2: note: in instantiation of member function 'ims::IntegerMassDecomposer<unsigned long, unsigned int>::fillExtendedResidueTable' requested here
fillExtendedResidueTable(alphabet, lcms, mass_in_lcms, infty, witness_vector, ertable);
^
imslib/src/ims/decomp/realmassdecomposer.cpp:22:12: note: in instantiation of member function 'ims::IntegerMassDecomposer<unsigned long, unsigned int>::IntegerMassDecomposer' requested here
new integer_decomposer_type(weights));
^
In file included from imslib/src/ims/decomp/realmassdecomposer.cpp:8:
In file included from ./imslib/src/ims/decomp/realmassdecomposer.h:7:
./imslib/src/ims/decomp/integermassdecomposer.h:230:18: warning: implicit conversion changes signedness: 'typename __normal_iterator<unsigned long *, vector<unsigned long, allocator<unsigned long> > >::difference_type' (aka 'long') to 'size_type' (aka 'unsigned long') [-Wsign-conversion]
_witnessVector[it - _ertable[1].begin()] = std::make_pair(witness, counter);
˜˜˜˜˜˜˜˜˜˜˜˜˜˜ ^˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜
./imslib/src/ims/decomp/integermassdecomposer.h:231:9: warning: implicit conversion changes signedness: 'size_type' (aka 'unsigned long') to 'const difference_type' (aka 'const long') [-Wsign-conversion]
it += it_inc;
˜˜ ^˜˜˜˜˜
./imslib/src/ims/decomp/integermassdecomposer.h:233:10: warning: implicit conversion changes signedness: 'size_type' (aka 'unsigned long') to 'const difference_type' (aka 'const long') [-Wsign-conversion]
it -= _ertable[1].size();
˜˜ ^˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜
./imslib/src/ims/decomp/integermassdecomposer.h:494:9: warning: implicit conversion loses integer precision: 'size_type' (aka 'unsigned long') to 'decomposition_value_type' (aka 'unsigned int') [-Wshorten-64-to-32]
return getAllDecompositions(mass).size();
˜˜˜˜˜˜ ^˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜
imslib/src/ims/decomp/realmassdecomposer.cpp:22:12: note: in instantiation of member function 'ims::IntegerMassDecomposer<unsigned long, unsigned int>::getNumberOfDecompositions' requested here
new integer_decomposer_type(weights));
^
11 warnings generated.
clang++ -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -I/usr/local/include -I"/Library/Frameworks/R.framework/Versions/3.0/Resources/library/RcppClassic/include" -I"/Library/Frameworks/R.framework/Versions/3.0/Resources/library/Rcpp/include" -I./imslib/src/ -fPIC -mtune=native -g -O2 -Wall -pedantic -Wconversion -c imslib/src/ims/utils/distribution.cpp -o imslib/src/ims/utils/distribution.o
clang++ -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -I/usr/local/include -I"/Library/Frameworks/R.framework/Versions/3.0/Resources/library/RcppClassic/include" -I"/Library/Frameworks/R.framework/Versions/3.0/Resources/library/Rcpp/include" -I./imslib/src/ -fPIC -mtune=native -g -O2 -Wall -pedantic -Wconversion -c imslib/src/ims/distributionprobabilityscorer.cpp -o imslib/src/ims/distributionprobabilityscorer.o
clang++ -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -I/usr/local/include -I"/Library/Frameworks/R.framework/Versions/3.0/Resources/library/RcppClassic/include" -I"/Library/Frameworks/R.framework/Versions/3.0/Resources/library/Rcpp/include" -I./imslib/src/ -fPIC -mtune=native -g -O2 -Wall -pedantic -Wconversion -c imslib/src/ims/characteralphabet.cpp -o imslib/src/ims/characteralphabet.o
In file included from imslib/src/ims/characteralphabet.cpp:3:
In file included from ./imslib/src/ims/characteralphabet.h:6:
In file included from imslib/src/ims/alphabet.h:8:
./imslib/src/ims/element.h:169:35: warning: implicit conversion changes signedness: 'int' to 'size_type' (aka 'unsigned long') [-Wsign-conversion]
if (isotopes.getAbundance(i) > 0.5) {
˜˜˜˜˜˜˜˜ ^
./imslib/src/ims/element.h:175:28: warning: implicit conversion changes signedness: 'int' to 'size_type' (aka 'unsigned long') [-Wsign-conversion]
return isotopes.getMass(i);
˜˜˜˜˜˜˜˜ ^
./imslib/src/ims/element.h:177:35: warning: implicit conversion changes signedness: 'int' to 'size_type' (aka 'unsigned long') [-Wsign-conversion]
if (isotopes.getAbundance(i) > maxval) {
˜˜˜˜˜˜˜˜ ^
./imslib/src/ims/element.h:178:35: warning: implicit conversion changes signedness: 'int' to 'size_type' (aka 'unsigned long') [-Wsign-conversion]
maxval = isotopes.getAbundance(i);
˜˜˜˜˜˜˜˜ ^
./imslib/src/ims/element.h:183:31: warning: implicit conversion changes signedness: 'int' to 'size_type' (aka 'unsigned long') [-Wsign-conversion]
return isotopes.getMass(maxindex);
˜˜˜˜˜˜˜˜ ^˜˜˜˜˜˜˜
5 warnings generated.
clang++ -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -I/usr/local/include -I"/Library/Frameworks/R.framework/Versions/3.0/Resources/library/RcppClassic/include" -I"/Library/Frameworks/R.framework/Versions/3.0/Resources/library/Rcpp/include" -I./imslib/src/ -fPIC -mtune=native -g -O2 -Wall -pedantic -Wconversion -c imslib/src/ims/nitrogenrulefilter.cpp -o imslib/src/ims/nitrogenrulefilter.o
In file included from imslib/src/ims/nitrogenrulefilter.cpp:5:
In file included from ./imslib/src/ims/nitrogenrulefilter.h:4:
In file included from ./imslib/src/ims/composedelement.h:7:
./imslib/src/ims/element.h:169:35: warning: implicit conversion changes signedness: 'int' to 'size_type' (aka 'unsigned long') [-Wsign-conversion]
if (isotopes.getAbundance(i) > 0.5) {
˜˜˜˜˜˜˜˜ ^
./imslib/src/ims/element.h:175:28: warning: implicit conversion changes signedness: 'int' to 'size_type' (aka 'unsigned long') [-Wsign-conversion]
return isotopes.getMass(i);
˜˜˜˜˜˜˜˜ ^
./imslib/src/ims/element.h:177:35: warning: implicit conversion changes signedness: 'int' to 'size_type' (aka 'unsigned long') [-Wsign-conversion]
if (isotopes.getAbundance(i) > maxval) {
˜˜˜˜˜˜˜˜ ^
./imslib/src/ims/element.h:178:35: warning: implicit conversion changes signedness: 'int' to 'size_type' (aka 'unsigned long') [-Wsign-conversion]
maxval = isotopes.getAbundance(i);
˜˜˜˜˜˜˜˜ ^
./imslib/src/ims/element.h:183:31: warning: implicit conversion changes signedness: 'int' to 'size_type' (aka 'unsigned long') [-Wsign-conversion]
return isotopes.getMass(maxindex);
˜˜˜˜˜˜˜˜ ^˜˜˜˜˜˜˜
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 Rdisop.so disop.o imslib/src/ims/element.o imslib/src/ims/composedelement.o imslib/src/ims/isotopedistribution.o imslib/src/ims/alphabet.o imslib/src/ims/weights.o imslib/src/ims/distributedalphabet.o imslib/src/ims/transformation.o imslib/src/ims/isotopespecies.o imslib/src/ims/base/parser/alphabettextparser.o imslib/src/ims/base/parser/distributedalphabettextparser.o imslib/src/ims/base/parser/massestextparser.o imslib/src/ims/base/parser/moleculesequenceparser.o imslib/src/ims/base/parser/standardmoleculesequenceparser.o imslib/src/ims/base/parser/keggligandcompoundsparser.o imslib/src/ims/base/parser/moleculeionchargemodificationparser.o imslib/src/ims/calib/linepairstabber.o imslib/src/ims/calib/matchmatrix.o imslib/src/ims/calib/linearpointsetmatcher.o imslib/src/ims/decomp/realmassdecomposer.o imslib/src/ims/utils/distribution.o imslib/src/ims/distributionprobabilityscorer.o imslib/src/ims/characteralphabet.o imslib/src/ims/nitrogenrulefilter.o /Library/Frameworks/R.framework/Versions/3.0/Resources/library/RcppClassic/lib/libRcppClassic.a /Library/Frameworks/R.framework/Versions/3.0/Resources/library/Rcpp/lib/libRcpp.a -F/Library/Frameworks/R.framework/.. -framework R -Wl,-framework -Wl,CoreFoundation
installing to /Users/biocbuild/bbs-2.12-bioc/meat/Rdisop.buildbin-libdir/Rdisop/libs
** R
** inst
** preparing package for lazy loading
** help
*** installing help indices
** building package indices
** installing vignettes
'Rdisop.Rnw'
** testing if installed package can be loaded
* DONE (Rdisop)
>>>>>>>
>>>>>>> FIXING LINKS FOR Rdisop.buildbin-libdir/Rdisop/libs//Rdisop.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" "Rdisop.buildbin-libdir/Rdisop/libs//Rdisop.so"
install_name_tool -change "/usr/local/lib/libgfortran.2.dylib" "/Library/Frameworks/R.framework/Versions/3.0/Resources/lib/libgfortran.2.dylib" "Rdisop.buildbin-libdir/Rdisop/libs//Rdisop.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" "Rdisop.buildbin-libdir/Rdisop/libs//Rdisop.so"
install_name_tool -change "/usr/local/lib/libreadline.dylib" "/Library/Frameworks/R.framework/Versions/3.0/Resources/lib/libreadline.dylib" "Rdisop.buildbin-libdir/Rdisop/libs//Rdisop.so"