* installing to library ‘/home/hornik/tmp/R.check/r-patched-gcc/Work/build/Packages’
* installing *source* package ‘AnaCoDa’ ...
** package ‘AnaCoDa’ successfully unpacked and MD5 sums checked
** using staged installation
checking whether the C++ compiler works... yes
checking for C++ compiler default output file name... a.out
checking for suffix of executables...
checking whether we are cross compiling... no
checking for suffix of object files... o
checking whether we are using the GNU C++ compiler... yes
checking whether g++-13 -std=gnu++11 accepts -g... yes
checking how to run the C++ preprocessor... g++-13 -std=gnu++11 -E
checking whether we are using the GNU C++ compiler... (cached) yes
checking whether g++-13 -std=gnu++11 accepts -g... (cached) yes
checking for gcc... gcc-13
checking whether we are using the GNU C compiler... yes
checking whether gcc-13 accepts -g... yes
checking for gcc-13 option to accept ISO C89... none needed
checking for g++-13 -std=gnu++11 option to support OpenMP... -fopenmp
checking for grep that handles long lines and -e... /usr/bin/grep
checking for egrep... /usr/bin/grep -E
checking for ANSI C header files... yes
checking for sys/types.h... yes
checking for sys/stat.h... yes
checking for stdlib.h... yes
checking for string.h... yes
checking for memory.h... yes
checking for strings.h... yes
checking for inttypes.h... yes
checking for stdint.h... yes
checking for unistd.h... yes
checking for stdlib.h... (cached) yes
checking for stdbool.h that conforms to C99... no
checking for _Bool... no
checking for inline... inline
checking for size_t... yes
checking for sqrt... yes
configure: creating ./config.status
config.status: creating src/Makevars
** libs
using C compiler: ‘gcc-13 (Debian 13.2.0-13) 13.2.0’
using C++ compiler: ‘g++-13 (Debian 13.2.0-13) 13.2.0’
using C++11
make[1]: Entering directory '/tmp/RtmpLpKITR/R.INSTALL27c9d555f96305/AnaCoDa/src'
g++-13 -std=gnu++11 -I"/home/hornik/tmp/R.check/r-patched-gcc/Work/build/include" -DNDEBUG -I'/home/hornik/tmp/R.check/r-patched-gcc/Work/build/Packages/Rcpp/include' -I/usr/local/include -D_FORTIFY_SOURCE=3 -fopenmp -fpic -g -O2 -Wall -pedantic -mtune=native -c CodonTable.cpp -o CodonTable.o
g++-13 -std=gnu++11 -I"/home/hornik/tmp/R.check/r-patched-gcc/Work/build/include" -DNDEBUG -I'/home/hornik/tmp/R.check/r-patched-gcc/Work/build/Packages/Rcpp/include' -I/usr/local/include -D_FORTIFY_SOURCE=3 -fopenmp -fpic -g -O2 -Wall -pedantic -mtune=native -c CovarianceMatrix.cpp -o CovarianceMatrix.o
g++-13 -std=gnu++11 -I"/home/hornik/tmp/R.check/r-patched-gcc/Work/build/include" -DNDEBUG -I'/home/hornik/tmp/R.check/r-patched-gcc/Work/build/Packages/Rcpp/include' -I/usr/local/include -D_FORTIFY_SOURCE=3 -fopenmp -fpic -g -O2 -Wall -pedantic -mtune=native -c FONSEModel.cpp -o FONSEModel.o
g++-13 -std=gnu++11 -I"/home/hornik/tmp/R.check/r-patched-gcc/Work/build/include" -DNDEBUG -I'/home/hornik/tmp/R.check/r-patched-gcc/Work/build/Packages/Rcpp/include' -I/usr/local/include -D_FORTIFY_SOURCE=3 -fopenmp -fpic -g -O2 -Wall -pedantic -mtune=native -c FONSEParameter.cpp -o FONSEParameter.o
g++-13 -std=gnu++11 -I"/home/hornik/tmp/R.check/r-patched-gcc/Work/build/include" -DNDEBUG -I'/home/hornik/tmp/R.check/r-patched-gcc/Work/build/Packages/Rcpp/include' -I/usr/local/include -D_FORTIFY_SOURCE=3 -fopenmp -fpic -g -O2 -Wall -pedantic -mtune=native -c Gene.cpp -o Gene.o
g++-13 -std=gnu++11 -I"/home/hornik/tmp/R.check/r-patched-gcc/Work/build/include" -DNDEBUG -I'/home/hornik/tmp/R.check/r-patched-gcc/Work/build/Packages/Rcpp/include' -I/usr/local/include -D_FORTIFY_SOURCE=3 -fopenmp -fpic -g -O2 -Wall -pedantic -mtune=native -c Genome.cpp -o Genome.o
g++-13 -std=gnu++11 -I"/home/hornik/tmp/R.check/r-patched-gcc/Work/build/include" -DNDEBUG -I'/home/hornik/tmp/R.check/r-patched-gcc/Work/build/Packages/Rcpp/include' -I/usr/local/include -D_FORTIFY_SOURCE=3 -fopenmp -fpic -g -O2 -Wall -pedantic -mtune=native -c MCMCAlgorithm.cpp -o MCMCAlgorithm.o
MCMCAlgorithm.cpp: In member function ‘double MCMCAlgorithm::acceptRejectSynthesisRateLevelForAllGenes(Genome&, Model&, int)’:
MCMCAlgorithm.cpp:112:33: warning: comparison of integer expressions of different signedness: ‘unsigned int’ and ‘int’ [-Wsign-compare]
112 | for (unsigned i = 0u; i < numGenes; i++)
| ~~^~~~~~~~~~
MCMCAlgorithm.cpp: In member function ‘void MCMCAlgorithm::run(Genome&, Model&, unsigned int, unsigned int)’:
MCMCAlgorithm.cpp:552:44: warning: comparison of integer expressions of different signedness: ‘int’ and ‘unsigned int’ [-Wsign-compare]
552 | for (int iteration = 1u; iteration <= maximumIterations; iteration++)
| ~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~
MCMCAlgorithm.cpp: In member function ‘void MCMCAlgorithm::run_PANSE(Genome&, PANSEModel&, unsigned int, unsigned int)’:
MCMCAlgorithm.cpp:701:44: warning: comparison of integer expressions of different signedness: ‘int’ and ‘unsigned int’ [-Wsign-compare]
701 | for (int iteration = 1u; iteration <= maximumIterations; iteration++)
| ~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~
MCMCAlgorithm.cpp: In static member function ‘static std::vector<std::vector<double> > MCMCAlgorithm::solveToeplitzMatrix(int, std::vector<double>, std::vector<double>)’:
MCMCAlgorithm.cpp:1239:32: warning: comparison of integer expressions of different signedness: ‘unsigned int’ and ‘int’ [-Wsign-compare]
1239 | for (unsigned l = 1; l < lr; l++)
| ~~^~~~
MCMCAlgorithm.cpp:1263:23: warning: comparison of integer expressions of different signedness: ‘unsigned int’ and ‘int’ [-Wsign-compare]
1263 | if (l == lr) return returnVec;
| ~~^~~~~
g++-13 -std=gnu++11 -I"/home/hornik/tmp/R.check/r-patched-gcc/Work/build/include" -DNDEBUG -I'/home/hornik/tmp/R.check/r-patched-gcc/Work/build/Packages/Rcpp/include' -I/usr/local/include -D_FORTIFY_SOURCE=3 -fopenmp -fpic -g -O2 -Wall -pedantic -mtune=native -c Model.cpp -o Model.o
g++-13 -std=gnu++11 -I"/home/hornik/tmp/R.check/r-patched-gcc/Work/build/include" -DNDEBUG -I'/home/hornik/tmp/R.check/r-patched-gcc/Work/build/Packages/Rcpp/include' -I/usr/local/include -D_FORTIFY_SOURCE=3 -fopenmp -fpic -g -O2 -Wall -pedantic -mtune=native -c PAModel.cpp -o PAModel.o
PAModel.cpp: In member function ‘virtual void PAModel::calculateZ(std::string, Genome&, std::vector<double>&)’:
PAModel.cpp:58:26: warning: unused variable ‘currNumCodonsInMRNA’ [-Wunused-variable]
58 | unsigned currNumCodonsInMRNA = gene->geneData.getCodonCountForCodon(codon);
| ^~~~~~~~~~~~~~~~~~~
g++-13 -std=gnu++11 -I"/home/hornik/tmp/R.check/r-patched-gcc/Work/build/include" -DNDEBUG -I'/home/hornik/tmp/R.check/r-patched-gcc/Work/build/Packages/Rcpp/include' -I/usr/local/include -D_FORTIFY_SOURCE=3 -fopenmp -fpic -g -O2 -Wall -pedantic -mtune=native -c PANSEModel.cpp -o PANSEModel.o
PANSEModel.cpp: In member function ‘virtual void PANSEModel::simulateGenome(Genome&)’:
PANSEModel.cpp:1255:18: warning: unused variable ‘lambdaCategory’ [-Wunused-variable]
1255 | unsigned lambdaCategory = parameter->getSelectionCategory(mixtureElement);
| ^~~~~~~~~~~~~~
g++-13 -std=gnu++11 -I"/home/hornik/tmp/R.check/r-patched-gcc/Work/build/include" -DNDEBUG -I'/home/hornik/tmp/R.check/r-patched-gcc/Work/build/Packages/Rcpp/include' -I/usr/local/include -D_FORTIFY_SOURCE=3 -fopenmp -fpic -g -O2 -Wall -pedantic -mtune=native -c PANSEParameter.cpp -o PANSEParameter.o
g++-13 -std=gnu++11 -I"/home/hornik/tmp/R.check/r-patched-gcc/Work/build/include" -DNDEBUG -I'/home/hornik/tmp/R.check/r-patched-gcc/Work/build/Packages/Rcpp/include' -I/usr/local/include -D_FORTIFY_SOURCE=3 -fopenmp -fpic -g -O2 -Wall -pedantic -mtune=native -c PAParameter.cpp -o PAParameter.o
g++-13 -std=gnu++11 -I"/home/hornik/tmp/R.check/r-patched-gcc/Work/build/include" -DNDEBUG -I'/home/hornik/tmp/R.check/r-patched-gcc/Work/build/Packages/Rcpp/include' -I/usr/local/include -D_FORTIFY_SOURCE=3 -fopenmp -fpic -g -O2 -Wall -pedantic -mtune=native -c Parameter.cpp -o Parameter.o
Parameter.cpp: In member function ‘void Parameter::adaptSynthesisRateProposalWidth(unsigned int, bool)’:
Parameter.cpp:1397:16: warning: unused variable ‘adjustFactor’ [-Wunused-variable]
1397 | double adjustFactor = 1.0; //variable assigned value of either adjustFactorLow or adjustFactorHigh depending on acceptance rate
| ^~~~~~~~~~~~
Parameter.cpp: In member function ‘std::vector<double> Parameter::getExpressionQuantile(unsigned int, unsigned int, std::vector<double>, bool)’:
Parameter.cpp:1988:35: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector<double>::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
1988 | for (int i = 0; i < probs.size();i++)
| ~~^~~~~~~~~~~~~~
g++-13 -std=gnu++11 -I"/home/hornik/tmp/R.check/r-patched-gcc/Work/build/include" -DNDEBUG -I'/home/hornik/tmp/R.check/r-patched-gcc/Work/build/Packages/Rcpp/include' -I/usr/local/include -D_FORTIFY_SOURCE=3 -fopenmp -fpic -g -O2 -Wall -pedantic -mtune=native -c RCPP_Model.cpp -o RCPP_Model.o
g++-13 -std=gnu++11 -I"/home/hornik/tmp/R.check/r-patched-gcc/Work/build/include" -DNDEBUG -I'/home/hornik/tmp/R.check/r-patched-gcc/Work/build/Packages/Rcpp/include' -I/usr/local/include -D_FORTIFY_SOURCE=3 -fopenmp -fpic -g -O2 -Wall -pedantic -mtune=native -c RCPP_Parameter.cpp -o RCPP_Parameter.o
g++-13 -std=gnu++11 -I"/home/hornik/tmp/R.check/r-patched-gcc/Work/build/include" -DNDEBUG -I'/home/hornik/tmp/R.check/r-patched-gcc/Work/build/Packages/Rcpp/include' -I/usr/local/include -D_FORTIFY_SOURCE=3 -fopenmp -fpic -g -O2 -Wall -pedantic -mtune=native -c RCPP_Trace.cpp -o RCPP_Trace.o
g++-13 -std=gnu++11 -I"/home/hornik/tmp/R.check/r-patched-gcc/Work/build/include" -DNDEBUG -I'/home/hornik/tmp/R.check/r-patched-gcc/Work/build/Packages/Rcpp/include' -I/usr/local/include -D_FORTIFY_SOURCE=3 -fopenmp -fpic -g -O2 -Wall -pedantic -mtune=native -c ROCModel.cpp -o ROCModel.o
ROCModel.cpp: In member function ‘virtual void ROCModel::calculateLogLikelihoodRatioPerGroupingPerCategory(std::string, Genome&, std::vector<double>&)’:
ROCModel.cpp:177:33: warning: comparison of integer expressions of different signedness: ‘unsigned int’ and ‘int’ [-Wsign-compare]
177 | for (unsigned i = 0u; i < numGenes; i++)
| ~~^~~~~~~~~~
g++-13 -std=gnu++11 -I"/home/hornik/tmp/R.check/r-patched-gcc/Work/build/include" -DNDEBUG -I'/home/hornik/tmp/R.check/r-patched-gcc/Work/build/Packages/Rcpp/include' -I/usr/local/include -D_FORTIFY_SOURCE=3 -fopenmp -fpic -g -O2 -Wall -pedantic -mtune=native -c ROCParameter.cpp -o ROCParameter.o
ROCParameter.cpp: In member function ‘void ROCParameter::initROCParameterSet()’:
ROCParameter.cpp:82:25: warning: comparison of integer expressions of different signedness: ‘int’ and ‘unsigned int’ [-Wsign-compare]
82 | for (int i=0; i < numMutationCategories; i++)
| ~~^~~~~~~~~~~~~~~~~~~~~~~
ROCParameter.cpp: In member function ‘void ROCParameter::initROCValuesFromFile(std::string)’:
ROCParameter.cpp:324:75: warning: comparison of integer expressions of different signedness: ‘int’ and ‘unsigned int’ [-Wsign-compare]
324 | for (int i = 0; i < numMutationCategories;i++)
| ~~^~~~~~~~~~~~~~~~~~~~~~~
ROCParameter.cpp:342:35: warning: comparison of integer expressions of different signedness: ‘int’ and ‘unsigned int’ [-Wsign-compare]
342 | for (int i = 0; i < numMutationCategories;i++)
| ~~^~~~~~~~~~~~~~~~~~~~~~~
g++-13 -std=gnu++11 -I"/home/hornik/tmp/R.check/r-patched-gcc/Work/build/include" -DNDEBUG -I'/home/hornik/tmp/R.check/r-patched-gcc/Work/build/Packages/Rcpp/include' -I/usr/local/include -D_FORTIFY_SOURCE=3 -fopenmp -fpic -g -O2 -Wall -pedantic -mtune=native -c SequenceSummary.cpp -o SequenceSummary.o
g++-13 -std=gnu++11 -I"/home/hornik/tmp/R.check/r-patched-gcc/Work/build/include" -DNDEBUG -I'/home/hornik/tmp/R.check/r-patched-gcc/Work/build/Packages/Rcpp/include' -I/usr/local/include -D_FORTIFY_SOURCE=3 -fopenmp -fpic -g -O2 -Wall -pedantic -mtune=native -c Testing.cpp -o Testing.o
Testing.cpp: In function ‘int testSequenceSummary()’:
Testing.cpp:874:22: warning: comparison of integer expressions of different signedness: ‘__gnu_cxx::__alloc_traits<std::allocator<unsigned int>, unsigned int>::value_type’ {aka ‘unsigned int’} and ‘int’ [-Wsign-compare]
874 | if (iVect[i] != tmp)
g++-13 -std=gnu++11 -I"/home/hornik/tmp/R.check/r-patched-gcc/Work/build/include" -DNDEBUG -I'/home/hornik/tmp/R.check/r-patched-gcc/Work/build/Packages/Rcpp/include' -I/usr/local/include -D_FORTIFY_SOURCE=3 -fopenmp -fpic -g -O2 -Wall -pedantic -mtune=native -c Trace.cpp -o Trace.o
g++-13 -std=gnu++11 -I"/home/hornik/tmp/R.check/r-patched-gcc/Work/build/include" -DNDEBUG -I'/home/hornik/tmp/R.check/r-patched-gcc/Work/build/Packages/Rcpp/include' -I/usr/local/include -D_FORTIFY_SOURCE=3 -fopenmp -fpic -g -O2 -Wall -pedantic -mtune=native -c main.cpp -o main.o
gcc-13 -I"/home/hornik/tmp/R.check/r-patched-gcc/Work/build/include" -DNDEBUG -I'/home/hornik/tmp/R.check/r-patched-gcc/Work/build/Packages/Rcpp/include' -I/usr/local/include -D_FORTIFY_SOURCE=3 -fpic -g -O2 -Wall -Wstrict-prototypes -pedantic -mtune=native -c registerDynamicSymbol.c -o registerDynamicSymbol.o
g++-13 -std=gnu++11 -shared -L/home/hornik/tmp/R.check/r-patched-gcc/Work/build/lib -Wl,-O1 -o AnaCoDa.so CodonTable.o CovarianceMatrix.o FONSEModel.o FONSEParameter.o Gene.o Genome.o MCMCAlgorithm.o Model.o PAModel.o PANSEModel.o PANSEParameter.o PAParameter.o Parameter.o RCPP_Model.o RCPP_Parameter.o RCPP_Trace.o ROCModel.o ROCParameter.o SequenceSummary.o Testing.o Trace.o main.o registerDynamicSymbol.o -fopenmp -L/home/hornik/tmp/R.check/r-patched-gcc/Work/build/lib -lR
make[1]: Leaving directory '/tmp/RtmpLpKITR/R.INSTALL27c9d555f96305/AnaCoDa/src'
make[1]: Entering directory '/tmp/RtmpLpKITR/R.INSTALL27c9d555f96305/AnaCoDa/src'
make[1]: Leaving directory '/tmp/RtmpLpKITR/R.INSTALL27c9d555f96305/AnaCoDa/src'
installing to /home/hornik/tmp/R.check/r-patched-gcc/Work/build/Packages/00LOCK-AnaCoDa/00new/AnaCoDa/libs
** R
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
converting help for package ‘AnaCoDa’
finding HTML links ... done
AAToCodon html
acfCSP html
acfMCMC html
addObservedSynthesisRateSet html
aminoAcids html
calculateMarginalLogLikelihood html
calculateSCUO html
codonToAA html
codons html
convergence.test html
findOptimalCodon html
fixDEta html
fixDM html
fixSphi html
geomMean html
getAdaptiveWidth html
getCAI html
getCAIweights html
getCSPEstimates html
getCodonCounts html
getCodonCountsForAA html
getCodonSpecificPosteriorMeanForCodon html
getCodonSpecificPosteriorVarianceForCodon
html
getCodonSpecificQuantilesForCodon html
getEstimatedMixtureAssignmentForGene html
getEstimatedMixtureAssignmentProbabilitiesForGene
html
getExpressionEstimates html
getGroupList html
getLogLikelihoodTrace html
getLogPosteriorMean html
getLogPosteriorTrace html
getMixtureAssignmentEstimate html
getNames html
getNc html
getNcAA html
getNoiseOffsetPosteriorMean html
getNoiseOffsetVariance html
getObservedSynthesisRateSet html
getSamples html
getSelectionCoefficients html
getStdDevSynthesisRatePosteriorMean html
getStdDevSynthesisRateVariance html
getStepsToAdapt html
getSynthesisRate html
getSynthesisRatePosteriorMeanForGene html
getSynthesisRatePosteriorVarianceForGene
html
getThinning html
getTrace html
getTraceObject html
initMutationCategories html
initSelectionCategories html
initializeCovarianceMatrices html
initializeGenomeObject html
initializeMCMCObject html
initializeModelObject html
initializeParameterObject html
initializeSynthesisRateByGenome html
initializeSynthesisRateByList html
initializeSynthesisRateByRandom html
length.Rcpp_Genome html
loadMCMCObject html
loadParameterObject html
plot.Rcpp_FONSEModel html
plot.Rcpp_FONSEParameter html
plot.Rcpp_MCMCAlgorithm html
plot.Rcpp_ROCModel html
plot.Rcpp_ROCParameter html
plot.Rcpp_Trace html
plotAcceptanceRatios html
plotCodonSpecificParameters html
readPhiValue html
runMCMC html
setAdaptiveWidth html
setGroupList html
setRestartFileSettings html
setRestartSettings html
setSamples html
setStepsToAdapt html
setThinning html
simulateGenome html
summary.Rcpp_Genome html
writeMCMCObject html
writeParameterObject html
** 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 (AnaCoDa)