* installing *source* package ‘mpMap2’ ...
** package ‘mpMap2’ successfully unpacked and MD5 sums checked
** using staged installation
** libs
make[2]: Entering directory '/data/gannet/ripley/R/packages/tests-noOMP/mpMap2/src'
/usr/local/clang-noOMP/bin/clang++ -std=gnu++11 -I"/data/gannet/ripley/R/R-clang-noOMP/include" -DNDEBUG  -I'/data/gannet/ripley/R/test-clang/Rcpp/include' -isystem /usr/local/clang/include  -I.  -fpic  -g -O3 -Wall -pedantic -frtti  -c alleleDataErrors.cpp -o alleleDataErrors.o
/usr/local/clang-noOMP/bin/clang++ -std=gnu++11 -I"/data/gannet/ripley/R/R-clang-noOMP/include" -DNDEBUG  -I'/data/gannet/ripley/R/test-clang/Rcpp/include' -isystem /usr/local/clang/include  -I.  -fpic  -g -O3 -Wall -pedantic -frtti  -c arsa.cpp -o arsa.o
/usr/local/clang-noOMP/bin/clang++ -std=gnu++11 -I"/data/gannet/ripley/R/R-clang-noOMP/include" -DNDEBUG  -I'/data/gannet/ripley/R/test-clang/Rcpp/include' -isystem /usr/local/clang/include  -I.  -fpic  -g -O3 -Wall -pedantic -frtti  -c arsaRaw.cpp -o arsaRaw.o
/usr/local/clang-noOMP/bin/clang++ -std=gnu++11 -I"/data/gannet/ripley/R/R-clang-noOMP/include" -DNDEBUG  -I'/data/gannet/ripley/R/test-clang/Rcpp/include' -isystem /usr/local/clang/include  -I.  -fpic  -g -O3 -Wall -pedantic -frtti  -c arsaRawREntryPoint.cpp -o arsaRawREntryPoint.o
/usr/local/clang-noOMP/bin/clang++ -std=gnu++11 -I"/data/gannet/ripley/R/R-clang-noOMP/include" -DNDEBUG  -I'/data/gannet/ripley/R/test-clang/Rcpp/include' -isystem /usr/local/clang/include  -I.  -fpic  -g -O3 -Wall -pedantic -frtti  -c assignFounderPattern.cpp -o assignFounderPattern.o
/usr/local/clang-noOMP/bin/clang++ -std=gnu++11 -I"/data/gannet/ripley/R/R-clang-noOMP/include" -DNDEBUG  -I'/data/gannet/ripley/R/test-clang/Rcpp/include' -isystem /usr/local/clang/include  -I.  -fpic  -g -O3 -Wall -pedantic -frtti  -c checkHets.cpp -o checkHets.o
/usr/local/clang-noOMP/bin/clang++ -std=gnu++11 -I"/data/gannet/ripley/R/R-clang-noOMP/include" -DNDEBUG  -I'/data/gannet/ripley/R/test-clang/Rcpp/include' -isystem /usr/local/clang/include  -I.  -fpic  -g -O3 -Wall -pedantic -frtti  -c checkImputedBounds.cpp -o checkImputedBounds.o
/usr/local/clang-noOMP/bin/clang++ -std=gnu++11 -I"/data/gannet/ripley/R/R-clang-noOMP/include" -DNDEBUG  -I'/data/gannet/ripley/R/test-clang/Rcpp/include' -isystem /usr/local/clang/include  -I.  -fpic  -g -O3 -Wall -pedantic -frtti  -c combineGenotypes.cpp -o combineGenotypes.o
/usr/local/clang-noOMP/bin/clang++ -std=gnu++11 -I"/data/gannet/ripley/R/R-clang-noOMP/include" -DNDEBUG  -I'/data/gannet/ripley/R/test-clang/Rcpp/include' -isystem /usr/local/clang/include  -I.  -fpic  -g -O3 -Wall -pedantic -frtti  -c combineRFDisjoint.cpp -o combineRFDisjoint.o
/usr/local/clang-noOMP/bin/clang++ -std=gnu++11 -I"/data/gannet/ripley/R/R-clang-noOMP/include" -DNDEBUG  -I'/data/gannet/ripley/R/test-clang/Rcpp/include' -isystem /usr/local/clang/include  -I.  -fpic  -g -O3 -Wall -pedantic -frtti  -c compressedProbabilities.cpp -o compressedProbabilities.o
/usr/local/clang-noOMP/bin/clang++ -std=gnu++11 -I"/data/gannet/ripley/R/R-clang-noOMP/include" -DNDEBUG  -I'/data/gannet/ripley/R/test-clang/Rcpp/include' -isystem /usr/local/clang/include  -I.  -fpic  -g -O3 -Wall -pedantic -frtti  -c compressedProbabilities_RInterface.cpp -o compressedProbabilities_RInterface.o
/usr/local/clang-noOMP/bin/clang++ -std=gnu++11 -I"/data/gannet/ripley/R/R-clang-noOMP/include" -DNDEBUG  -I'/data/gannet/ripley/R/test-clang/Rcpp/include' -isystem /usr/local/clang/include  -I.  -fpic  -g -O3 -Wall -pedantic -frtti  -c computeAllEpistaticChiSquared.cpp -o computeAllEpistaticChiSquared.o
/usr/local/clang-noOMP/bin/clang++ -std=gnu++11 -I"/data/gannet/ripley/R/R-clang-noOMP/include" -DNDEBUG  -I'/data/gannet/ripley/R/test-clang/Rcpp/include' -isystem /usr/local/clang/include  -I.  -fpic  -g -O3 -Wall -pedantic -frtti  -c computeGenotypeProbabilities.cpp -o computeGenotypeProbabilities.o
/usr/local/clang-noOMP/bin/clang++ -std=gnu++11 -I"/data/gannet/ripley/R/R-clang-noOMP/include" -DNDEBUG  -I'/data/gannet/ripley/R/test-clang/Rcpp/include' -isystem /usr/local/clang/include  -I.  -fpic  -g -O3 -Wall -pedantic -frtti  -c convertGeneticData.cpp -o convertGeneticData.o
/usr/local/clang-noOMP/bin/clang++ -std=gnu++11 -I"/data/gannet/ripley/R/R-clang-noOMP/include" -DNDEBUG  -I'/data/gannet/ripley/R/test-clang/Rcpp/include' -isystem /usr/local/clang/include  -I.  -fpic  -g -O3 -Wall -pedantic -frtti  -c crc32.cpp -o crc32.o
/usr/local/clang-noOMP/bin/clang++ -std=gnu++11 -I"/data/gannet/ripley/R/R-clang-noOMP/include" -DNDEBUG  -I'/data/gannet/ripley/R/test-clang/Rcpp/include' -isystem /usr/local/clang/include  -I.  -fpic  -g -O3 -Wall -pedantic -frtti  -c dspMatrix.cpp -o dspMatrix.o
/usr/local/clang-noOMP/bin/clang++ -std=gnu++11 -I"/data/gannet/ripley/R/R-clang-noOMP/include" -DNDEBUG  -I'/data/gannet/ripley/R/test-clang/Rcpp/include' -isystem /usr/local/clang/include  -I.  -fpic  -g -O3 -Wall -pedantic -frtti  -c eightParentPedigreeImproperFunnels.cpp -o eightParentPedigreeImproperFunnels.o
/usr/local/clang-noOMP/bin/clang++ -std=gnu++11 -I"/data/gannet/ripley/R/R-clang-noOMP/include" -DNDEBUG  -I'/data/gannet/ripley/R/test-clang/Rcpp/include' -isystem /usr/local/clang/include  -I.  -fpic  -g -O3 -Wall -pedantic -frtti  -c eightParentPedigreeRandomFunnels.cpp -o eightParentPedigreeRandomFunnels.o
/usr/local/clang-noOMP/bin/clang++ -std=gnu++11 -I"/data/gannet/ripley/R/R-clang-noOMP/include" -DNDEBUG  -I'/data/gannet/ripley/R/test-clang/Rcpp/include' -isystem /usr/local/clang/include  -I.  -fpic  -g -O3 -Wall -pedantic -frtti  -c eightParentPedigreeSingleFunnel.cpp -o eightParentPedigreeSingleFunnel.o
/usr/local/clang-noOMP/bin/clang++ -std=gnu++11 -I"/data/gannet/ripley/R/R-clang-noOMP/include" -DNDEBUG  -I'/data/gannet/ripley/R/test-clang/Rcpp/include' -isystem /usr/local/clang/include  -I.  -fpic  -g -O3 -Wall -pedantic -frtti  -c estimateRF.cpp -o estimateRF.o
/usr/local/clang-noOMP/bin/clang++ -std=gnu++11 -I"/data/gannet/ripley/R/R-clang-noOMP/include" -DNDEBUG  -I'/data/gannet/ripley/R/test-clang/Rcpp/include' -isystem /usr/local/clang/include  -I.  -fpic  -g -O3 -Wall -pedantic -frtti  -c estimateRFCheckFunnels.cpp -o estimateRFCheckFunnels.o
/usr/local/clang-noOMP/bin/clang++ -std=gnu++11 -I"/data/gannet/ripley/R/R-clang-noOMP/include" -DNDEBUG  -I'/data/gannet/ripley/R/test-clang/Rcpp/include' -isystem /usr/local/clang/include  -I.  -fpic  -g -O3 -Wall -pedantic -frtti  -c estimateRFSingleDesign.cpp -o estimateRFSingleDesign.o
/usr/local/clang-noOMP/bin/clang++ -std=gnu++11 -I"/data/gannet/ripley/R/R-clang-noOMP/include" -DNDEBUG  -I'/data/gannet/ripley/R/test-clang/Rcpp/include' -isystem /usr/local/clang/include  -I.  -fpic  -g -O3 -Wall -pedantic -frtti  -c estimateRFSingleDesignInternal.cpp -o estimateRFSingleDesignInternal.o
/usr/local/clang-noOMP/bin/clang++ -std=gnu++11 -I"/data/gannet/ripley/R/R-clang-noOMP/include" -DNDEBUG  -I'/data/gannet/ripley/R/test-clang/Rcpp/include' -isystem /usr/local/clang/include  -I.  -fpic  -g -O3 -Wall -pedantic -frtti  -c estimateRFSpecificDesign.cpp -o estimateRFSpecificDesign.o
/usr/local/clang-noOMP/bin/clang++ -std=gnu++11 -I"/data/gannet/ripley/R/R-clang-noOMP/include" -DNDEBUG  -I'/data/gannet/ripley/R/test-clang/Rcpp/include' -isystem /usr/local/clang/include  -I.  -fpic  -g -O3 -Wall -pedantic -frtti  -c expandedProbabilities_RInterface.cpp -o expandedProbabilities_RInterface.o
/usr/local/clang-noOMP/bin/clang++ -std=gnu++11 -I"/data/gannet/ripley/R/R-clang-noOMP/include" -DNDEBUG  -I'/data/gannet/ripley/R/test-clang/Rcpp/include' -isystem /usr/local/clang/include  -I.  -fpic  -g -O3 -Wall -pedantic -frtti  -c fourParentPedigreeRandomFunnels.cpp -o fourParentPedigreeRandomFunnels.o
/usr/local/clang-noOMP/bin/clang++ -std=gnu++11 -I"/data/gannet/ripley/R/R-clang-noOMP/include" -DNDEBUG  -I'/data/gannet/ripley/R/test-clang/Rcpp/include' -isystem /usr/local/clang/include  -I.  -fpic  -g -O3 -Wall -pedantic -frtti  -c fourParentPedigreeSingleFunnel.cpp -o fourParentPedigreeSingleFunnel.o
/usr/local/clang-noOMP/bin/clang++ -std=gnu++11 -I"/data/gannet/ripley/R/R-clang-noOMP/include" -DNDEBUG  -I'/data/gannet/ripley/R/test-clang/Rcpp/include' -isystem /usr/local/clang/include  -I.  -fpic  -g -O3 -Wall -pedantic -frtti  -c funnelsToUniqueValues.cpp -o funnelsToUniqueValues.o
/usr/local/clang-noOMP/bin/clang++ -std=gnu++11 -I"/data/gannet/ripley/R/R-clang-noOMP/include" -DNDEBUG  -I'/data/gannet/ripley/R/test-clang/Rcpp/include' -isystem /usr/local/clang/include  -I.  -fpic  -g -O3 -Wall -pedantic -frtti  -c generateDesignMatrix.cpp -o generateDesignMatrix.o
/usr/local/clang-noOMP/bin/clang++ -std=gnu++11 -I"/data/gannet/ripley/R/R-clang-noOMP/include" -DNDEBUG  -I'/data/gannet/ripley/R/test-clang/Rcpp/include' -isystem /usr/local/clang/include  -I.  -fpic  -g -O3 -Wall -pedantic -frtti  -c generateGenotypes.cpp -o generateGenotypes.o
/usr/local/clang-noOMP/bin/clang++ -std=gnu++11 -I"/data/gannet/ripley/R/R-clang-noOMP/include" -DNDEBUG  -I'/data/gannet/ripley/R/test-clang/Rcpp/include' -isystem /usr/local/clang/include  -I.  -fpic  -g -O3 -Wall -pedantic -frtti  -c generateKeys.cpp -o generateKeys.o
/usr/local/clang-noOMP/bin/clang++ -std=gnu++11 -I"/data/gannet/ripley/R/R-clang-noOMP/include" -DNDEBUG  -I'/data/gannet/ripley/R/test-clang/Rcpp/include' -isystem /usr/local/clang/include  -I.  -fpic  -g -O3 -Wall -pedantic -frtti  -c getAllFunnels.cpp -o getAllFunnels.o
/usr/local/clang-noOMP/bin/clang++ -std=gnu++11 -I"/data/gannet/ripley/R/R-clang-noOMP/include" -DNDEBUG  -I'/data/gannet/ripley/R/test-clang/Rcpp/include' -isystem /usr/local/clang/include  -I.  -fpic  -g -O3 -Wall -pedantic -frtti  -c getAllFunnelsIncAIC.cpp -o getAllFunnelsIncAIC.o
/usr/local/clang-noOMP/bin/clang++ -std=gnu++11 -I"/data/gannet/ripley/R/R-clang-noOMP/include" -DNDEBUG  -I'/data/gannet/ripley/R/test-clang/Rcpp/include' -isystem /usr/local/clang/include  -I.  -fpic  -g -O3 -Wall -pedantic -frtti  -c getFunnel.cpp -o getFunnel.o
/usr/local/clang-noOMP/bin/clang++ -std=gnu++11 -I"/data/gannet/ripley/R/R-clang-noOMP/include" -DNDEBUG  -I'/data/gannet/ripley/R/test-clang/Rcpp/include' -isystem /usr/local/clang/include  -I.  -fpic  -g -O3 -Wall -pedantic -frtti  -c getMinAIGenerations.cpp -o getMinAIGenerations.o
/usr/local/clang-noOMP/bin/clang++ -std=gnu++11 -I"/data/gannet/ripley/R/R-clang-noOMP/include" -DNDEBUG  -I'/data/gannet/ripley/R/test-clang/Rcpp/include' -isystem /usr/local/clang/include  -I.  -fpic  -g -O3 -Wall -pedantic -frtti  -c haldaneToRf.cpp -o haldaneToRf.o
/usr/local/clang-noOMP/bin/clang++ -std=gnu++11 -I"/data/gannet/ripley/R/R-clang-noOMP/include" -DNDEBUG  -I'/data/gannet/ripley/R/test-clang/Rcpp/include' -isystem /usr/local/clang/include  -I.  -fpic  -g -O3 -Wall -pedantic -frtti  -c hclustMatrices.cpp -o hclustMatrices.o
/usr/local/clang-noOMP/bin/clang++ -std=gnu++11 -I"/data/gannet/ripley/R/R-clang-noOMP/include" -DNDEBUG  -I'/data/gannet/ripley/R/test-clang/Rcpp/include' -isystem /usr/local/clang/include  -I.  -fpic  -g -O3 -Wall -pedantic -frtti  -c identC.cpp -o identC.o
/usr/local/clang-noOMP/bin/clang++ -std=gnu++11 -I"/data/gannet/ripley/R/R-clang-noOMP/include" -DNDEBUG  -I'/data/gannet/ripley/R/test-clang/Rcpp/include' -isystem /usr/local/clang/include  -I.  -fpic  -g -O3 -Wall -pedantic -frtti  -c impute.cpp -o impute.o
/usr/local/clang-noOMP/bin/clang++ -std=gnu++11 -I"/data/gannet/ripley/R/R-clang-noOMP/include" -DNDEBUG  -I'/data/gannet/ripley/R/test-clang/Rcpp/include' -isystem /usr/local/clang/include  -I.  -fpic  -g -O3 -Wall -pedantic -frtti  -c imputeFounders.cpp -o imputeFounders.o
estimateRFSpecificDesign.cpp:65:7: error: unknown type name 'omp_loop_type'
                for(omp_loop_type counter = 0; counter < (omp_loop_type)pairsToEstimate.size(); counter++)
                    ^
estimateRFSpecificDesign.cpp:65:45: error: use of undeclared identifier 'omp_loop_type'
                for(omp_loop_type counter = 0; counter < (omp_loop_type)pairsToEstimate.size(); counter++)
                                                          ^
/usr/local/clang-noOMP/bin/clang++ -std=gnu++11 -I"/data/gannet/ripley/R/R-clang-noOMP/include" -DNDEBUG  -I'/data/gannet/ripley/R/test-clang/Rcpp/include' -isystem /usr/local/clang/include  -I.  -fpic  -g -O3 -Wall -pedantic -frtti  -c intercrossingAndSelfingGenerations.cpp -o intercrossingAndSelfingGenerations.o
estimateRFSpecificDesign.cpp:176:7: error: unknown type name 'omp_loop_type'
                for(omp_loop_type counter = 0; counter < (omp_loop_type)pairsToEstimate.size(); counter++)
                    ^
estimateRFSpecificDesign.cpp:176:45: error: use of undeclared identifier 'omp_loop_type'
                for(omp_loop_type counter = 0; counter < (omp_loop_type)pairsToEstimate.size(); counter++)
                                                          ^
/usr/local/clang-noOMP/bin/clang++ -std=gnu++11 -I"/data/gannet/ripley/R/R-clang-noOMP/include" -DNDEBUG  -I'/data/gannet/ripley/R/test-clang/Rcpp/include' -isystem /usr/local/clang/include  -I.  -fpic  -g -O3 -Wall -pedantic -frtti  -c joinMapWithExtra.cpp -o joinMapWithExtra.o
/usr/local/clang-noOMP/bin/clang++ -std=gnu++11 -I"/data/gannet/ripley/R/R-clang-noOMP/include" -DNDEBUG  -I'/data/gannet/ripley/R/test-clang/Rcpp/include' -isystem /usr/local/clang/include  -I.  -fpic  -g -O3 -Wall -pedantic -frtti  -c mapFunctions.cpp -o mapFunctions.o
/usr/local/clang-noOMP/bin/clang++ -std=gnu++11 -I"/data/gannet/ripley/R/R-clang-noOMP/include" -DNDEBUG  -I'/data/gannet/ripley/R/test-clang/Rcpp/include' -isystem /usr/local/clang/include  -I.  -fpic  -g -O3 -Wall -pedantic -frtti  -c markerPatternsToUniqueValues.cpp -o markerPatternsToUniqueValues.o
/usr/local/clang-noOMP/bin/clang++ -std=gnu++11 -I"/data/gannet/ripley/R/R-clang-noOMP/include" -DNDEBUG  -I'/data/gannet/ripley/R/test-clang/Rcpp/include' -isystem /usr/local/clang/include  -I.  -fpic  -g -O3 -Wall -pedantic -frtti  -c matrixChunks.cpp -o matrixChunks.o
/usr/local/clang-noOMP/bin/clang++ -std=gnu++11 -I"/data/gannet/ripley/R/R-clang-noOMP/include" -DNDEBUG  -I'/data/gannet/ripley/R/test-clang/Rcpp/include' -isystem /usr/local/clang/include  -I.  -fpic  -g -O3 -Wall -pedantic -frtti  -c mpMap2_openmp.cpp -o mpMap2_openmp.o
/usr/local/clang-noOMP/bin/clang++ -std=gnu++11 -I"/data/gannet/ripley/R/R-clang-noOMP/include" -DNDEBUG  -I'/data/gannet/ripley/R/test-clang/Rcpp/include' -isystem /usr/local/clang/include  -I.  -fpic  -g -O3 -Wall -pedantic -frtti  -c multiparentSNP.cpp -o multiparentSNP.o
/usr/local/clang-noOMP/bin/clang++ -std=gnu++11 -I"/data/gannet/ripley/R/R-clang-noOMP/include" -DNDEBUG  -I'/data/gannet/ripley/R/test-clang/Rcpp/include' -isystem /usr/local/clang/include  -I.  -fpic  -g -O3 -Wall -pedantic -frtti  -c order.cpp -o order.o
/usr/local/clang-noOMP/bin/clang++ -std=gnu++11 -I"/data/gannet/ripley/R/R-clang-noOMP/include" -DNDEBUG  -I'/data/gannet/ripley/R/test-clang/Rcpp/include' -isystem /usr/local/clang/include  -I.  -fpic  -g -O3 -Wall -pedantic -frtti  -c orderFunnel.cpp -o orderFunnel.o
/usr/local/clang-noOMP/bin/clang++ -std=gnu++11 -I"/data/gannet/ripley/R/R-clang-noOMP/include" -DNDEBUG  -I'/data/gannet/ripley/R/test-clang/Rcpp/include' -isystem /usr/local/clang/include  -I.  -fpic  -g -O3 -Wall -pedantic -frtti  -c parsePurdy.cpp -o parsePurdy.o
/usr/local/clang-noOMP/bin/clang++ -std=gnu++11 -I"/data/gannet/ripley/R/R-clang-noOMP/include" -DNDEBUG  -I'/data/gannet/ripley/R/test-clang/Rcpp/include' -isystem /usr/local/clang/include  -I.  -fpic  -g -O3 -Wall -pedantic -frtti  -c preClusterStep.cpp -o preClusterStep.o
/usr/local/clang-noOMP/bin/clang++ -std=gnu++11 -I"/data/gannet/ripley/R/R-clang-noOMP/include" -DNDEBUG  -I'/data/gannet/ripley/R/test-clang/Rcpp/include' -isystem /usr/local/clang/include  -I.  -fpic  -g -O3 -Wall -pedantic -frtti  -c probabilities16.cpp -o probabilities16.o
/usr/local/clang-noOMP/bin/clang++ -std=gnu++11 -I"/data/gannet/ripley/R/R-clang-noOMP/include" -DNDEBUG  -I'/data/gannet/ripley/R/test-clang/Rcpp/include' -isystem /usr/local/clang/include  -I.  -fpic  -g -O3 -Wall -pedantic -frtti  -c probabilities2.cpp -o probabilities2.o
/usr/local/clang-noOMP/bin/clang++ -std=gnu++11 -I"/data/gannet/ripley/R/R-clang-noOMP/include" -DNDEBUG  -I'/data/gannet/ripley/R/test-clang/Rcpp/include' -isystem /usr/local/clang/include  -I.  -fpic  -g -O3 -Wall -pedantic -frtti  -c probabilities4.cpp -o probabilities4.o
/usr/local/clang-noOMP/bin/clang++ -std=gnu++11 -I"/data/gannet/ripley/R/R-clang-noOMP/include" -DNDEBUG  -I'/data/gannet/ripley/R/test-clang/Rcpp/include' -isystem /usr/local/clang/include  -I.  -fpic  -g -O3 -Wall -pedantic -frtti  -c probabilities8.cpp -o probabilities8.o
/usr/local/clang-noOMP/bin/clang++ -std=gnu++11 -I"/data/gannet/ripley/R/R-clang-noOMP/include" -DNDEBUG  -I'/data/gannet/ripley/R/test-clang/Rcpp/include' -isystem /usr/local/clang/include  -I.  -fpic  -g -O3 -Wall -pedantic -frtti  -c rawSymmetricMatrix.cpp -o rawSymmetricMatrix.o
/usr/local/clang-noOMP/bin/clang++ -std=gnu++11 -I"/data/gannet/ripley/R/R-clang-noOMP/include" -DNDEBUG  -I'/data/gannet/ripley/R/test-clang/Rcpp/include' -isystem /usr/local/clang/include  -I.  -fpic  -g -O3 -Wall -pedantic -frtti  -c recodeFoundersFinalsHets.cpp -o recodeFoundersFinalsHets.o
/usr/local/clang-noOMP/bin/clang++ -std=gnu++11 -I"/data/gannet/ripley/R/R-clang-noOMP/include" -DNDEBUG  -I'/data/gannet/ripley/R/test-clang/Rcpp/include' -isystem /usr/local/clang/include  -I.  -fpic  -g -O3 -Wall -pedantic -frtti  -c register.cpp -o register.o
/usr/local/clang-noOMP/bin/clang++ -std=gnu++11 -I"/data/gannet/ripley/R/R-clang-noOMP/include" -DNDEBUG  -I'/data/gannet/ripley/R/test-clang/Rcpp/include' -isystem /usr/local/clang/include  -I.  -fpic  -g -O3 -Wall -pedantic -frtti  -c removeHets.cpp -o removeHets.o
/usr/local/clang-noOMP/bin/clang++ -std=gnu++11 -I"/data/gannet/ripley/R/R-clang-noOMP/include" -DNDEBUG  -I'/data/gannet/ripley/R/test-clang/Rcpp/include' -isystem /usr/local/clang/include  -I.  -fpic  -g -O3 -Wall -pedantic -frtti  -c reorderPedigree.cpp -o reorderPedigree.o
/usr/local/clang-noOMP/bin/clang++ -std=gnu++11 -I"/data/gannet/ripley/R/R-clang-noOMP/include" -DNDEBUG  -I'/data/gannet/ripley/R/test-clang/Rcpp/include' -isystem /usr/local/clang/include  -I.  -fpic  -g -O3 -Wall -pedantic -frtti  -c replaceHetsWithNA.cpp -o replaceHetsWithNA.o
/usr/local/clang-noOMP/bin/clang++ -std=gnu++11 -I"/data/gannet/ripley/R/R-clang-noOMP/include" -DNDEBUG  -I'/data/gannet/ripley/R/test-clang/Rcpp/include' -isystem /usr/local/clang/include  -I.  -fpic  -g -O3 -Wall -pedantic -frtti  -c singleLocusProbabilities_RInterface.cpp -o singleLocusProbabilities_RInterface.o
/usr/local/clang-noOMP/bin/clang++ -std=gnu++11 -I"/data/gannet/ripley/R/R-clang-noOMP/include" -DNDEBUG  -I'/data/gannet/ripley/R/test-clang/Rcpp/include' -isystem /usr/local/clang/include  -I.  -fpic  -g -O3 -Wall -pedantic -frtti  -c sixteenParentPedigreeRandomFunnels.cpp -o sixteenParentPedigreeRandomFunnels.o
/usr/local/clang-noOMP/bin/clang++ -std=gnu++11 -I"/data/gannet/ripley/R/R-clang-noOMP/include" -DNDEBUG  -I'/data/gannet/ripley/R/test-clang/Rcpp/include' -isystem /usr/local/clang/include  -I.  -fpic  -g -O3 -Wall -pedantic -frtti  -c sortPedigreeLineNames.cpp -o sortPedigreeLineNames.o
/usr/local/clang-noOMP/bin/clang++ -std=gnu++11 -I"/data/gannet/ripley/R/R-clang-noOMP/include" -DNDEBUG  -I'/data/gannet/ripley/R/test-clang/Rcpp/include' -isystem /usr/local/clang/include  -I.  -fpic  -g -O3 -Wall -pedantic -frtti  -c stripPedigree.cpp -o stripPedigree.o
/usr/local/clang-noOMP/bin/clang++ -std=gnu++11 -I"/data/gannet/ripley/R/R-clang-noOMP/include" -DNDEBUG  -I'/data/gannet/ripley/R/test-clang/Rcpp/include' -isystem /usr/local/clang/include  -I.  -fpic  -g -O3 -Wall -pedantic -frtti  -c testDistortion.cpp -o testDistortion.o
/usr/local/clang-noOMP/bin/clang++ -std=gnu++11 -I"/data/gannet/ripley/R/R-clang-noOMP/include" -DNDEBUG  -I'/data/gannet/ripley/R/test-clang/Rcpp/include' -isystem /usr/local/clang/include  -I.  -fpic  -g -O3 -Wall -pedantic -frtti  -c throwInternal.cpp -o throwInternal.o
/usr/local/clang-noOMP/bin/clang++ -std=gnu++11 -I"/data/gannet/ripley/R/R-clang-noOMP/include" -DNDEBUG  -I'/data/gannet/ripley/R/test-clang/Rcpp/include' -isystem /usr/local/clang/include  -I.  -fpic  -g -O3 -Wall -pedantic -frtti  -c transformForMPWGAIM.cpp -o transformForMPWGAIM.o
/usr/local/clang-noOMP/bin/clang++ -std=gnu++11 -I"/data/gannet/ripley/R/R-clang-noOMP/include" -DNDEBUG  -I'/data/gannet/ripley/R/test-clang/Rcpp/include' -isystem /usr/local/clang/include  -I.  -fpic  -g -O3 -Wall -pedantic -frtti  -c transposeProbabilities.cpp -o transposeProbabilities.o
4 errors generated.
make[2]: *** [/data/gannet/ripley/R/R-clang-noOMP/etc/Makeconf:175: estimateRFSpecificDesign.o] Error 1
/usr/local/clang-noOMP/bin/clang++ -std=gnu++11 -I"/data/gannet/ripley/R/R-clang-noOMP/include" -DNDEBUG  -I'/data/gannet/ripley/R/test-clang/Rcpp/include' -isystem /usr/local/clang/include  -I.  -fpic  -g -O3 -Wall -pedantic -frtti  -c warnings.cpp -o warnings.o
make[2]: Target 'all' not remade because of errors.
make[2]: Leaving directory '/data/gannet/ripley/R/packages/tests-noOMP/mpMap2/src'
ERROR: compilation failed for package ‘mpMap2’
* removing ‘/data/gannet/ripley/R/packages/tests-noOMP/mpMap2.Rcheck/mpMap2’