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Package 531/671HostnameOS / ArchBUILDCHECKBUILD BIN
Rdisop 1.20.0
Steffen Neumann
Snapshot Date: 2013-04-30 17:01:37 -0700 (Tue, 30 Apr 2013)
URL: https://hedgehog.fhcrc.org/bioconductor/branches/RELEASE_2_12/madman/Rpacks/Rdisop
Last Changed Rev: 75263 / Revision: 76155
Last Changed Date: 2013-04-03 14:32:27 -0700 (Wed, 03 Apr 2013)
george2 Linux (Ubuntu 12.04.1 LTS) / x86_64  OK  OK 
moscato2 Windows Server 2008 R2 Enterprise SP1 (64-bit) / x64  OK  OK  OK 
petty Mac OS X Snow Leopard (10.6.8) / x86_64  OK  OK  OK 
pelham Mac OS X Snow Leopard (10.6.8) / x86_64  OK  OK [ OK ]

Summary

Package: Rdisop
Version: 1.20.0
Command: rm -rf Rdisop.buildbin-libdir && mkdir Rdisop.buildbin-libdir && /Users/biocbuild/BBS/utils/build-universal.sh Rdisop_1.20.0.tar.gz /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R Rdisop.buildbin-libdir
StartedAt: 2013-05-01 12:47:58 -0700 (Wed, 01 May 2013)
EndedAt: 2013-05-01 12:48:35 -0700 (Wed, 01 May 2013)
EllapsedTime: 36.7 seconds
RetCode: 0
Status:  OK 
PackageFile: Rdisop_1.20.0.tgz
PackageFileSize: 412.8 KiB

Command output

>>>>>>> 
>>>>>>> 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'.
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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'.
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make: *** No rule to make target `tests/base/parser/.deps/moleculesequenceparsertest.Po'.
make: *** No rule to make target `tests/base/parser/.deps/massestextparsertest.Po'.
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make: *** No rule to make target `tests/.deps/shifttransformationtest.Po'.
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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'.
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make: *** No rule to make target `tests/.deps/masspeaktest.Po'.
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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'.
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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"