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###
### Running command:
###
### rm -rf Aerith.buildbin-libdir && mkdir Aerith.buildbin-libdir && /Users/biocbuild/BBS/utils/build-universal.sh Aerith_0.99.11.tar.gz /Library/Frameworks/R.framework/Resources/bin/R Aerith.buildbin-libdir
###
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>>>>>>>
>>>>>>> INSTALLATION WITH 'R CMD INSTALL --preclean --no-multiarch --library=Aerith.buildbin-libdir Aerith_0.99.11.tar.gz'
>>>>>>>
* installing *source* package ‘Aerith’ ...
** this is package ‘Aerith’ version ‘0.99.11’
** using staged installation
** libs
specified C++17
using C++ compiler: ‘Apple clang version 17.0.0 (clang-1700.6.4.2)’
using C++17
using SDK: ‘MacOSX26.2.sdk’
clang++ -arch arm64 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I. -I'/Library/Frameworks/R.framework/Versions/4.6/Resources/library/Rcpp/include' -I/opt/R/arm64/include -fPIC -falign-functions=64 -Wall -g -O2 -c RcppExports.cpp -o RcppExports.o
clang++ -arch arm64 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I. -I'/Library/Frameworks/R.framework/Versions/4.6/Resources/library/Rcpp/include' -I/opt/R/arm64/include -fPIC -falign-functions=64 -Wall -g -O2 -c extractPSMfeatures.cpp -o extractPSMfeatures.o
clang++ -arch arm64 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I. -I'/Library/Frameworks/R.framework/Versions/4.6/Resources/library/Rcpp/include' -I/opt/R/arm64/include -fPIC -falign-functions=64 -Wall -g -O2 -c filterPSMs.cpp -o filterPSMs.o
filterPSMs.cpp:23:48: warning: unqualified call to 'std::move' [-Wunqualified-std-cast-call]
23 | return DataFrame::create(Named("psmIDs") = move(msipPSMinfo.psmIDs),
| ^
| std::
filterPSMs.cpp:24:49: warning: unqualified call to 'std::move' [-Wunqualified-std-cast-call]
24 | _("ftFileNames") = move(msipPSMinfo.fileNames),
| ^
| std::
filterPSMs.cpp:25:49: warning: unqualified call to 'std::move' [-Wunqualified-std-cast-call]
25 | _["scanNumbers"] = move(msipPSMinfo.scanNumbers),
| ^
| std::
filterPSMs.cpp:26:52: warning: unqualified call to 'std::move' [-Wunqualified-std-cast-call]
26 | _["retentionTimes"] = move(msipPSMinfo.retentionTimes),
| ^
| std::
filterPSMs.cpp:27:44: warning: unqualified call to 'std::move' [-Wunqualified-std-cast-call]
27 | _["scores"] = move(msipPSMinfo.scores),
| ^
| std::
filterPSMs.cpp:28:43: warning: unqualified call to 'std::move' [-Wunqualified-std-cast-call]
28 | _["ranks"] = move(msipPSMinfo.ranks),
| ^
| std::
filterPSMs.cpp:29:51: warning: unqualified call to 'std::move' [-Wunqualified-std-cast-call]
29 | _["parentCharges"] = move(msipPSMinfo.parentCharges),
| ^
| std::
filterPSMs.cpp:30:42: warning: unqualified call to 'std::move' [-Wunqualified-std-cast-call]
30 | _["pcts"] = move(msipPSMinfo.pcts),
| ^
| std::
filterPSMs.cpp:31:49: warning: unqualified call to 'std::move' [-Wunqualified-std-cast-call]
31 | _["searchNames"] = move(msipPSMinfo.searchNames),
| ^
| std::
filterPSMs.cpp:32:46: warning: unqualified call to 'std::move' [-Wunqualified-std-cast-call]
32 | _["isDecoys"] = move(msipPSMinfo.isDecoys),
| ^
| std::
filterPSMs.cpp:33:58: warning: unqualified call to 'std::move' [-Wunqualified-std-cast-call]
33 | _["measuredParentMasses"] = move(msipPSMinfo.measuredParentMasses),
| ^
| std::
filterPSMs.cpp:34:60: warning: unqualified call to 'std::move' [-Wunqualified-std-cast-call]
34 | _["calculatedParentMasses"] = move(msipPSMinfo.calculatedParentMasses),
| ^
| std::
filterPSMs.cpp:35:55: warning: unqualified call to 'std::move' [-Wunqualified-std-cast-call]
35 | _["identifiedPepSeqs"] = move(msipPSMinfo.identifiedPeptides),
| ^
| std::
filterPSMs.cpp:36:53: warning: unqualified call to 'std::move' [-Wunqualified-std-cast-call]
36 | _["originalPepSeqs"] = move(msipPSMinfo.originalPeptides),
| ^
| std::
filterPSMs.cpp:37:49: warning: unqualified call to 'std::move' [-Wunqualified-std-cast-call]
37 | _["realPepSeqs"] = move(msipPSMinfo.realPepSeqs),
| ^
| std::
filterPSMs.cpp:38:53: warning: unqualified call to 'std::move' [-Wunqualified-std-cast-call]
38 | _["formatedPepSeqs"] = move(msipPSMinfo.formatedPepSeqs),
| ^
| std::
filterPSMs.cpp:39:48: warning: unqualified call to 'std::move' [-Wunqualified-std-cast-call]
39 | _["pepLengths"] = move(msipPSMinfo.pepLengths),
| ^
| std::
filterPSMs.cpp:40:46: warning: unqualified call to 'std::move' [-Wunqualified-std-cast-call]
40 | _["proNames"] = move(msipPSMinfo.proteinNames),
| ^
| std::
filterPSMs.cpp:41:56: warning: unqualified call to 'std::move' [-Wunqualified-std-cast-call]
41 | _["trimedProteinNames"] = move(msipPSMinfo.trimedProteinNames),
| ^
| std::
filterPSMs.cpp:42:47: warning: unqualified call to 'std::move' [-Wunqualified-std-cast-call]
42 | _["proCounts"] = move(msipPSMinfo.proCounts));
| ^
| std::
20 warnings generated.
clang++ -arch arm64 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I. -I'/Library/Frameworks/R.framework/Versions/4.6/Resources/library/Rcpp/include' -I/opt/R/arm64/include -fPIC -falign-functions=64 -Wall -g -O2 -c filterPeptides.cpp -o filterPeptides.o
filterPeptides.cpp:34:60: warning: unqualified call to 'std::move' [-Wunqualified-std-cast-call]
34 | return DataFrame::create(Named("identifiedPeptides") = move(identifiedPeptides),
| ^
| std::
filterPeptides.cpp:35:48: warning: unqualified call to 'std::move' [-Wunqualified-std-cast-call]
35 | _["bestScores"] = move(bestScores),
| ^
| std::
filterPeptides.cpp:36:45: warning: unqualified call to 'std::move' [-Wunqualified-std-cast-call]
36 | _["isDecoy"] = move(isDecoy));
| ^
| std::
filterPeptides.cpp:85:62: warning: unqualified call to 'std::move' [-Wunqualified-std-cast-call]
85 | DataFrame psmDf = DataFrame::create(Named("fileNames") = move(topPSMs.fileNames),
| ^
| std::
filterPeptides.cpp:86:60: warning: unqualified call to 'std::move' [-Wunqualified-std-cast-call]
86 | _["scanNumbers"] = move(topPSMs.scanNumbers),
| ^
| std::
filterPeptides.cpp:87:62: warning: unqualified call to 'std::move' [-Wunqualified-std-cast-call]
87 | _["parentCharges"] = move(topPSMs.parentCharges),
| ^
| std::
filterPeptides.cpp:88:69: warning: unqualified call to 'std::move' [-Wunqualified-std-cast-call]
88 | _["measuredParentMasses"] = move(topPSMs.measuredParentMasses),
| ^
| std::
filterPeptides.cpp:89:71: warning: unqualified call to 'std::move' [-Wunqualified-std-cast-call]
89 | _["calculatedParentMasses"] = move(topPSMs.calculatedParentMasses),
| ^
| std::
filterPeptides.cpp:90:60: warning: unqualified call to 'std::move' [-Wunqualified-std-cast-call]
90 | _["searchNames"] = move(topPSMs.searchNames),
| ^
| std::
filterPeptides.cpp:91:55: warning: unqualified call to 'std::move' [-Wunqualified-std-cast-call]
91 | _["scores"] = move(topPSMs.scores),
| ^
| std::
filterPeptides.cpp:92:67: warning: unqualified call to 'std::move' [-Wunqualified-std-cast-call]
92 | _["identifiedPeptides"] = move(topPSMs.identifiedPeptides),
| ^
| std::
filterPeptides.cpp:93:65: warning: unqualified call to 'std::move' [-Wunqualified-std-cast-call]
93 | _["originalPeptides"] = move(topPSMs.originalPeptides),
| ^
| std::
filterPeptides.cpp:94:61: warning: unqualified call to 'std::move' [-Wunqualified-std-cast-call]
94 | _["proteinNames"] = move(topPSMs.proteinNames));
| ^
| std::
13 warnings generated.
clang++ -arch arm64 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I. -I'/Library/Frameworks/R.framework/Versions/4.6/Resources/library/Rcpp/include' -I/opt/R/arm64/include -fPIC -falign-functions=64 -Wall -g -O2 -c generateCFG.cpp -o generateCFG.o
clang++ -arch arm64 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I. -I'/Library/Frameworks/R.framework/Versions/4.6/Resources/library/Rcpp/include' -I/opt/R/arm64/include -fPIC -falign-functions=64 -Wall -g -O2 -c getISOpeak.cpp -o getISOpeak.o
getISOpeak.cpp:344:39: warning: unqualified call to 'std::move' [-Wunqualified-std-cast-call]
344 | DataFrame::create(Named("Mass") = move(mSIP.vMass), _["Prob"] = move(mSIP.vProb));
| ^
| std::
getISOpeak.cpp:344:69: warning: unqualified call to 'std::move' [-Wunqualified-std-cast-call]
344 | DataFrame::create(Named("Mass") = move(mSIP.vMass), _["Prob"] = move(mSIP.vProb));
| ^
| std::
getISOpeak.cpp:345:21: warning: unqualified call to 'std::move' [-Wunqualified-std-cast-call]
345 | spectraList[i] = move(df);
| ^
| std::
getISOpeak.cpp:400:37: warning: unqualified call to 'std::move' [-Wunqualified-std-cast-call]
400 | DataFrame::create(Named("Mass") = move(masses),
| ^
| std::
getISOpeak.cpp:401:21: warning: unqualified call to 'std::move' [-Wunqualified-std-cast-call]
401 | _["Prob"] = move(probs), _["Kind"] = move(kinds));
| ^
| std::
getISOpeak.cpp:401:46: warning: unqualified call to 'std::move' [-Wunqualified-std-cast-call]
401 | _["Prob"] = move(probs), _["Kind"] = move(kinds));
| ^
| std::
6 warnings generated.
clang++ -arch arm64 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I. -I'/Library/Frameworks/R.framework/Versions/4.6/Resources/library/Rcpp/include' -I/opt/R/arm64/include -fPIC -falign-functions=64 -Wall -g -O2 -c readScan.cpp -o readScan.o
clang++ -arch arm64 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I. -I'/Library/Frameworks/R.framework/Versions/4.6/Resources/library/Rcpp/include' -I/opt/R/arm64/include -fPIC -falign-functions=64 -Wall -g -O2 -c readScans.cpp -o readScans.o
readScans.cpp:138:65: warning: unqualified call to 'std::move' [-Wunqualified-std-cast-call]
138 | DataFrame peakDf = DataFrame::create(Named("mz") = wrap(move(mScan->mz)),
| ^
| std::
readScans.cpp:139:68: warning: unqualified call to 'std::move' [-Wunqualified-std-cast-call]
139 | _["intensity"] = wrap(move(mScan->intensity)),
| ^
| std::
readScans.cpp:140:69: warning: unqualified call to 'std::move' [-Wunqualified-std-cast-call]
140 | _["resolution"] = wrap(move(mScan->resolution)),
| ^
| std::
readScans.cpp:141:67: warning: unqualified call to 'std::move' [-Wunqualified-std-cast-call]
141 | _["baseLine"] = wrap(move(mScan->baseLine)),
| ^
| std::
readScans.cpp:142:72: warning: unqualified call to 'std::move' [-Wunqualified-std-cast-call]
142 | _["signalToNoise"] = wrap(move(mScan->signalToNoise)),
| ^
| std::
readScans.cpp:143:65: warning: unqualified call to 'std::move' [-Wunqualified-std-cast-call]
143 | _["charge"] = wrap(move(mScan->charge)));
| ^
| std::
readScans.cpp:270:65: warning: unqualified call to 'std::move' [-Wunqualified-std-cast-call]
270 | DataFrame peakDf = DataFrame::create(Named("mz") = wrap(move(mScan->mz)),
| ^
| std::
readScans.cpp:271:68: warning: unqualified call to 'std::move' [-Wunqualified-std-cast-call]
271 | _["intensity"] = wrap(move(mScan->intensity)),
| ^
| std::
readScans.cpp:272:69: warning: unqualified call to 'std::move' [-Wunqualified-std-cast-call]
272 | _["resolution"] = wrap(move(mScan->resolution)),
| ^
| std::
readScans.cpp:273:67: warning: unqualified call to 'std::move' [-Wunqualified-std-cast-call]
273 | _["baseLine"] = wrap(move(mScan->baseLine)),
| ^
| std::
readScans.cpp:274:72: warning: unqualified call to 'std::move' [-Wunqualified-std-cast-call]
274 | _["signalToNoise"] = wrap(move(mScan->signalToNoise)),
| ^
| std::
readScans.cpp:275:65: warning: unqualified call to 'std::move' [-Wunqualified-std-cast-call]
275 | _["charge"] = wrap(move(mScan->charge)));
| ^
| std::
12 warnings generated.
clang++ -arch arm64 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I. -I'/Library/Frameworks/R.framework/Versions/4.6/Resources/library/Rcpp/include' -I/opt/R/arm64/include -fPIC -falign-functions=64 -Wall -g -O2 -c readSips.cpp -o readSips.o
clang++ -arch arm64 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I. -I'/Library/Frameworks/R.framework/Versions/4.6/Resources/library/Rcpp/include' -I/opt/R/arm64/include -fPIC -falign-functions=64 -Wall -g -O2 -c readSpe2Peps.cpp -o readSpe2Peps.o
clang++ -arch arm64 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I. -I'/Library/Frameworks/R.framework/Versions/4.6/Resources/library/Rcpp/include' -I/opt/R/arm64/include -fPIC -falign-functions=64 -Wall -g -O2 -c scorePSM.cpp -o scorePSM.o
scorePSM.cpp:431:22: warning: variable 'ibeginPos' is uninitialized when passed as a const reference argument here [-Wuninitialized-const-reference]
431 | ibeginPos, dPeptideMass, cIdentifyPrefix,
| ^~~~~~~~~
scorePSM.cpp:431:33: warning: variable 'dPeptideMass' is uninitialized when passed as a const reference argument here [-Wuninitialized-const-reference]
431 | ibeginPos, dPeptideMass, cIdentifyPrefix,
| ^~~~~~~~~~~~
scorePSM.cpp:431:47: warning: variable 'cIdentifyPrefix' is uninitialized when passed as a const reference argument here [-Wuninitialized-const-reference]
431 | ibeginPos, dPeptideMass, cIdentifyPrefix,
| ^~~~~~~~~~~~~~~
scorePSM.cpp:432:22: warning: variable 'cIdentifySuffix' is uninitialized when passed as a const reference argument here [-Wuninitialized-const-reference]
432 | cIdentifySuffix, cOriginalPrefix, cOriginalSuffix);
| ^~~~~~~~~~~~~~~
scorePSM.cpp:432:39: warning: variable 'cOriginalPrefix' is uninitialized when passed as a const reference argument here [-Wuninitialized-const-reference]
432 | cIdentifySuffix, cOriginalPrefix, cOriginalSuffix);
| ^~~~~~~~~~~~~~~
scorePSM.cpp:432:56: warning: variable 'cOriginalSuffix' is uninitialized when passed as a const reference argument here [-Wuninitialized-const-reference]
432 | cIdentifySuffix, cOriginalPrefix, cOriginalSuffix);
| ^~~~~~~~~~~~~~~
scorePSM.cpp:578:22: warning: variable 'ibeginPos' is uninitialized when passed as a const reference argument here [-Wuninitialized-const-reference]
578 | ibeginPos, dPeptideMass, cIdentifyPrefix,
| ^~~~~~~~~
scorePSM.cpp:578:33: warning: variable 'dPeptideMass' is uninitialized when passed as a const reference argument here [-Wuninitialized-const-reference]
578 | ibeginPos, dPeptideMass, cIdentifyPrefix,
| ^~~~~~~~~~~~
scorePSM.cpp:578:47: warning: variable 'cIdentifyPrefix' is uninitialized when passed as a const reference argument here [-Wuninitialized-const-reference]
578 | ibeginPos, dPeptideMass, cIdentifyPrefix,
| ^~~~~~~~~~~~~~~
scorePSM.cpp:579:22: warning: variable 'cIdentifySuffix' is uninitialized when passed as a const reference argument here [-Wuninitialized-const-reference]
579 | cIdentifySuffix, cOriginalPrefix, cOriginalSuffix);
| ^~~~~~~~~~~~~~~
scorePSM.cpp:579:39: warning: variable 'cOriginalPrefix' is uninitialized when passed as a const reference argument here [-Wuninitialized-const-reference]
579 | cIdentifySuffix, cOriginalPrefix, cOriginalSuffix);
| ^~~~~~~~~~~~~~~
scorePSM.cpp:579:56: warning: variable 'cOriginalSuffix' is uninitialized when passed as a const reference argument here [-Wuninitialized-const-reference]
579 | cIdentifySuffix, cOriginalPrefix, cOriginalSuffix);
| ^~~~~~~~~~~~~~~
12 warnings generated.
clang++ -arch arm64 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I. -I'/Library/Frameworks/R.framework/Versions/4.6/Resources/library/Rcpp/include' -I/opt/R/arm64/include -fPIC -falign-functions=64 -Wall -g -O2 -c writeScans.cpp -o writeScans.o
clang++ -arch arm64 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I. -I'/Library/Frameworks/R.framework/Versions/4.6/Resources/library/Rcpp/include' -I/opt/R/arm64/include -fPIC -falign-functions=64 -Wall -g -O2 -c lib/PSMfeatureExtractor.cpp -o lib/PSMfeatureExtractor.o
clang++ -arch arm64 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I. -I'/Library/Frameworks/R.framework/Versions/4.6/Resources/library/Rcpp/include' -I/opt/R/arm64/include -fPIC -falign-functions=64 -Wall -g -O2 -c lib/PSMpeakAnnotator.cpp -o lib/PSMpeakAnnotator.o
clang++ -arch arm64 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I. -I'/Library/Frameworks/R.framework/Versions/4.6/Resources/library/Rcpp/include' -I/opt/R/arm64/include -fPIC -falign-functions=64 -Wall -g -O2 -c lib/PSMsFiltrator.cpp -o lib/PSMsFiltrator.o
clang++ -arch arm64 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I. -I'/Library/Frameworks/R.framework/Versions/4.6/Resources/library/Rcpp/include' -I/opt/R/arm64/include -fPIC -falign-functions=64 -Wall -g -O2 -c lib/Spe2PepFileReader.cpp -o lib/Spe2PepFileReader.o
clang++ -arch arm64 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I. -I'/Library/Frameworks/R.framework/Versions/4.6/Resources/library/Rcpp/include' -I/opt/R/arm64/include -fPIC -falign-functions=64 -Wall -g -O2 -c lib/averagine.cpp -o lib/averagine.o
clang++ -arch arm64 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I. -I'/Library/Frameworks/R.framework/Versions/4.6/Resources/library/Rcpp/include' -I/opt/R/arm64/include -fPIC -falign-functions=64 -Wall -g -O2 -c lib/cfgParser.cpp -o lib/cfgParser.o
clang++ -arch arm64 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I. -I'/Library/Frameworks/R.framework/Versions/4.6/Resources/library/Rcpp/include' -I/opt/R/arm64/include -fPIC -falign-functions=64 -Wall -g -O2 -c lib/ftFileReader.cpp -o lib/ftFileReader.o
clang++ -arch arm64 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I. -I'/Library/Frameworks/R.framework/Versions/4.6/Resources/library/Rcpp/include' -I/opt/R/arm64/include -fPIC -falign-functions=64 -Wall -g -O2 -c lib/ftFileWriter.cpp -o lib/ftFileWriter.o
clang++ -arch arm64 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I. -I'/Library/Frameworks/R.framework/Versions/4.6/Resources/library/Rcpp/include' -I/opt/R/arm64/include -fPIC -falign-functions=64 -Wall -g -O2 -c lib/isotopologue.cpp -o lib/isotopologue.o
clang++ -arch arm64 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I. -I'/Library/Frameworks/R.framework/Versions/4.6/Resources/library/Rcpp/include' -I/opt/R/arm64/include -fPIC -falign-functions=64 -Wall -g -O2 -c lib/ms2scan.cpp -o lib/ms2scan.o
clang++ -arch arm64 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I. -I'/Library/Frameworks/R.framework/Versions/4.6/Resources/library/Rcpp/include' -I/opt/R/arm64/include -fPIC -falign-functions=64 -Wall -g -O2 -c lib/peptide.cpp -o lib/peptide.o
clang++ -arch arm64 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I. -I'/Library/Frameworks/R.framework/Versions/4.6/Resources/library/Rcpp/include' -I/opt/R/arm64/include -fPIC -falign-functions=64 -Wall -g -O2 -c lib/peptidesFiltrator.cpp -o lib/peptidesFiltrator.o
clang++ -arch arm64 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I. -I'/Library/Frameworks/R.framework/Versions/4.6/Resources/library/Rcpp/include' -I/opt/R/arm64/include -fPIC -falign-functions=64 -Wall -g -O2 -c lib/proNovoConfig.cpp -o lib/proNovoConfig.o
clang++ -arch arm64 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I. -I'/Library/Frameworks/R.framework/Versions/4.6/Resources/library/Rcpp/include' -I/opt/R/arm64/include -fPIC -falign-functions=64 -Wall -g -O2 -c lib/sipFileReader.cpp -o lib/sipFileReader.o
clang++ -arch arm64 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I. -I'/Library/Frameworks/R.framework/Versions/4.6/Resources/library/Rcpp/include' -I/opt/R/arm64/include -fPIC -falign-functions=64 -Wall -g -O2 -c lib/sipGenerator.cpp -o lib/sipGenerator.o
clang++ -arch arm64 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I. -I'/Library/Frameworks/R.framework/Versions/4.6/Resources/library/Rcpp/include' -I/opt/R/arm64/include -fPIC -falign-functions=64 -Wall -g -O2 -c lib/sipPSM.cpp -o lib/sipPSM.o
clang++ -arch arm64 -std=gnu++17 -dynamiclib -Wl,-headerpad_max_install_names -undefined dynamic_lookup -L/Library/Frameworks/R.framework/Resources/lib -L/opt/R/arm64/lib -o Aerith.so RcppExports.o extractPSMfeatures.o filterPSMs.o filterPeptides.o generateCFG.o getISOpeak.o readScan.o readScans.o readSips.o readSpe2Peps.o scorePSM.o writeScans.o lib/PSMfeatureExtractor.o lib/PSMpeakAnnotator.o lib/PSMsFiltrator.o lib/Spe2PepFileReader.o lib/averagine.o lib/cfgParser.o lib/ftFileReader.o lib/ftFileWriter.o lib/isotopologue.o lib/ms2scan.o lib/peptide.o lib/peptidesFiltrator.o lib/proNovoConfig.o lib/sipFileReader.o lib/sipGenerator.o lib/sipPSM.o -F/Library/Frameworks/R.framework/.. -framework R
installing to /Users/biocbuild/bbs-3.23-bioc/meat/Aerith.buildbin-libdir/00LOCK-Aerith/00new/Aerith/libs
** R
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded from temporary location
** checking absolute paths in shared objects and dynamic libraries
** testing if installed package can be loaded from final location
** testing if installed package keeps a record of temporary installation path
* DONE (Aerith)
>>>>>>>
>>>>>>> FIXING PATHS TO DYNAMIC LIBRARIES FOR Aerith.buildbin-libdir/Aerith/libs/Aerith.so
>>>>>>>
>>>>>>> Paths before fix:
Aerith.buildbin-libdir/Aerith/libs/Aerith.so:
Aerith.so (compatibility version 0.0.0, current version 0.0.0)
/Library/Frameworks/R.framework/Versions/4.6/Resources/lib/libR.dylib (compatibility version 4.6.0, current version 4.6.0)
/usr/lib/libc++.1.dylib (compatibility version 1.0.0, current version 2000.67.0)
/usr/lib/libSystem.B.dylib (compatibility version 1.0.0, current version 1356.0.0)
>>>>>>> Fix with install_name_tool:
install_name_tool -change "/usr/local/lib/libgcc_s.1.1.dylib" "/Library/Frameworks/R.framework/Versions/4.6/Resources/lib/libgcc_s.1.1.dylib" "Aerith.buildbin-libdir/Aerith/libs/Aerith.so"
install_name_tool -change "/usr/local/lib/libgfortran.5.dylib" "/Library/Frameworks/R.framework/Versions/4.6/Resources/lib/libgfortran.5.dylib" "Aerith.buildbin-libdir/Aerith/libs/Aerith.so"
install_name_tool -change "/usr/local/lib/libquadmath.0.dylib" "/Library/Frameworks/R.framework/Versions/4.6/Resources/lib/libquadmath.0.dylib" "Aerith.buildbin-libdir/Aerith/libs/Aerith.so"
>>>>>>> Paths after fix:
Aerith.buildbin-libdir/Aerith/libs/Aerith.so:
Aerith.so (compatibility version 0.0.0, current version 0.0.0)
/Library/Frameworks/R.framework/Versions/4.6/Resources/lib/libR.dylib (compatibility version 4.6.0, current version 4.6.0)
/usr/lib/libc++.1.dylib (compatibility version 1.0.0, current version 2000.67.0)
/usr/lib/libSystem.B.dylib (compatibility version 1.0.0, current version 1356.0.0)
