* installing to library ‘/home/hornik/tmp/R.check/r-patched-gcc/Work/build/Packages’
* installing *source* package ‘BLMEngineInR’ ...
** this is package ‘BLMEngineInR’ version ‘0.1.7’
** package ‘BLMEngineInR’ successfully unpacked and MD5 sums checked
** using staged installation
** libs
using C++ compiler: ‘g++-14 (Debian 14.3.0-8) 14.3.0’
make[1]: Entering directory '/home/hornik/tmp/scratch/RtmphIvizQ/R.INSTALL1418c037fb97a3/BLMEngineInR/src'
g++-14 -std=gnu++17 -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'/home/hornik/tmp/R.check/r-patched-gcc/Work/build/Packages/RcppArmadillo/include' -I/usr/local/include -D_FORTIFY_SOURCE=3 -fopenmp -DARMA_USE_LEGACY -fpic -g -O2 -Wall -pedantic -mtune=native -c AdjustForToxMode.cpp -o AdjustForToxMode.o
g++-14 -std=gnu++17 -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'/home/hornik/tmp/R.check/r-patched-gcc/Work/build/Packages/RcppArmadillo/include' -I/usr/local/include -D_FORTIFY_SOURCE=3 -fopenmp -DARMA_USE_LEGACY -fpic -g -O2 -Wall -pedantic -mtune=native -c AdjustForWHAM.cpp -o AdjustForWHAM.o
g++-14 -std=gnu++17 -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'/home/hornik/tmp/R.check/r-patched-gcc/Work/build/Packages/RcppArmadillo/include' -I/usr/local/include -D_FORTIFY_SOURCE=3 -fopenmp -DARMA_USE_LEGACY -fpic -g -O2 -Wall -pedantic -mtune=native -c CHESS.cpp -o CHESS.o
g++-14 -std=gnu++17 -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'/home/hornik/tmp/R.check/r-patched-gcc/Work/build/Packages/RcppArmadillo/include' -I/usr/local/include -D_FORTIFY_SOURCE=3 -fopenmp -DARMA_USE_LEGACY -fpic -g -O2 -Wall -pedantic -mtune=native -c CHESSIter.cpp -o CHESSIter.o
g++-14 -std=gnu++17 -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'/home/hornik/tmp/R.check/r-patched-gcc/Work/build/Packages/RcppArmadillo/include' -I/usr/local/include -D_FORTIFY_SOURCE=3 -fopenmp -DARMA_USE_LEGACY -fpic -g -O2 -Wall -pedantic -mtune=native -c CalcActivityCoef.cpp -o CalcActivityCoef.o
g++-14 -std=gnu++17 -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'/home/hornik/tmp/R.check/r-patched-gcc/Work/build/Packages/RcppArmadillo/include' -I/usr/local/include -D_FORTIFY_SOURCE=3 -fopenmp -DARMA_USE_LEGACY -fpic -g -O2 -Wall -pedantic -mtune=native -c CalcChargeBalance.cpp -o CalcChargeBalance.o
g++-14 -std=gnu++17 -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'/home/hornik/tmp/R.check/r-patched-gcc/Work/build/Packages/RcppArmadillo/include' -I/usr/local/include -D_FORTIFY_SOURCE=3 -fopenmp -DARMA_USE_LEGACY -fpic -g -O2 -Wall -pedantic -mtune=native -c CalcDonnanLayer.cpp -o CalcDonnanLayer.o
g++-14 -std=gnu++17 -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'/home/hornik/tmp/R.check/r-patched-gcc/Work/build/Packages/RcppArmadillo/include' -I/usr/local/include -D_FORTIFY_SOURCE=3 -fopenmp -DARMA_USE_LEGACY -fpic -g -O2 -Wall -pedantic -mtune=native -c CalcIonicStrength.cpp -o CalcIonicStrength.o
g++-14 -std=gnu++17 -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'/home/hornik/tmp/R.check/r-patched-gcc/Work/build/Packages/RcppArmadillo/include' -I/usr/local/include -D_FORTIFY_SOURCE=3 -fopenmp -DARMA_USE_LEGACY -fpic -g -O2 -Wall -pedantic -mtune=native -c CalcIonicStrengthEffects.cpp -o CalcIonicStrengthEffects.o
g++-14 -std=gnu++17 -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'/home/hornik/tmp/R.check/r-patched-gcc/Work/build/Packages/RcppArmadillo/include' -I/usr/local/include -D_FORTIFY_SOURCE=3 -fopenmp -DARMA_USE_LEGACY -fpic -g -O2 -Wall -pedantic -mtune=native -c CalcIterationTotalMoles.cpp -o CalcIterationTotalMoles.o
g++-14 -std=gnu++17 -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'/home/hornik/tmp/R.check/r-patched-gcc/Work/build/Packages/RcppArmadillo/include' -I/usr/local/include -D_FORTIFY_SOURCE=3 -fopenmp -DARMA_USE_LEGACY -fpic -g -O2 -Wall -pedantic -mtune=native -c CalcIterationTotals.cpp -o CalcIterationTotals.o
g++-14 -std=gnu++17 -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'/home/hornik/tmp/R.check/r-patched-gcc/Work/build/Packages/RcppArmadillo/include' -I/usr/local/include -D_FORTIFY_SOURCE=3 -fopenmp -DARMA_USE_LEGACY -fpic -g -O2 -Wall -pedantic -mtune=native -c CalcResidAndError.cpp -o CalcResidAndError.o
g++-14 -std=gnu++17 -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'/home/hornik/tmp/R.check/r-patched-gcc/Work/build/Packages/RcppArmadillo/include' -I/usr/local/include -D_FORTIFY_SOURCE=3 -fopenmp -DARMA_USE_LEGACY -fpic -g -O2 -Wall -pedantic -mtune=native -c CalcSpecConc.cpp -o CalcSpecConc.o
g++-14 -std=gnu++17 -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'/home/hornik/tmp/R.check/r-patched-gcc/Work/build/Packages/RcppArmadillo/include' -I/usr/local/include -D_FORTIFY_SOURCE=3 -fopenmp -DARMA_USE_LEGACY -fpic -g -O2 -Wall -pedantic -mtune=native -c CalcStep.cpp -o CalcStep.o
g++-14 -std=gnu++17 -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'/home/hornik/tmp/R.check/r-patched-gcc/Work/build/Packages/RcppArmadillo/include' -I/usr/local/include -D_FORTIFY_SOURCE=3 -fopenmp -DARMA_USE_LEGACY -fpic -g -O2 -Wall -pedantic -mtune=native -c CalcWHAMSpecCharge.cpp -o CalcWHAMSpecCharge.o
g++-14 -std=gnu++17 -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'/home/hornik/tmp/R.check/r-patched-gcc/Work/build/Packages/RcppArmadillo/include' -I/usr/local/include -D_FORTIFY_SOURCE=3 -fopenmp -DARMA_USE_LEGACY -fpic -g -O2 -Wall -pedantic -mtune=native -c CompUpdate.cpp -o CompUpdate.o
g++-14 -std=gnu++17 -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'/home/hornik/tmp/R.check/r-patched-gcc/Work/build/Packages/RcppArmadillo/include' -I/usr/local/include -D_FORTIFY_SOURCE=3 -fopenmp -DARMA_USE_LEGACY -fpic -g -O2 -Wall -pedantic -mtune=native -c InitialGuess.cpp -o InitialGuess.o
g++-14 -std=gnu++17 -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'/home/hornik/tmp/R.check/r-patched-gcc/Work/build/Packages/RcppArmadillo/include' -I/usr/local/include -D_FORTIFY_SOURCE=3 -fopenmp -DARMA_USE_LEGACY -fpic -g -O2 -Wall -pedantic -mtune=native -c Jacobian.cpp -o Jacobian.o
g++-14 -std=gnu++17 -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'/home/hornik/tmp/R.check/r-patched-gcc/Work/build/Packages/RcppArmadillo/include' -I/usr/local/include -D_FORTIFY_SOURCE=3 -fopenmp -DARMA_USE_LEGACY -fpic -g -O2 -Wall -pedantic -mtune=native -c MaxCompError.cpp -o MaxCompError.o
g++-14 -std=gnu++17 -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'/home/hornik/tmp/R.check/r-patched-gcc/Work/build/Packages/RcppArmadillo/include' -I/usr/local/include -D_FORTIFY_SOURCE=3 -fopenmp -DARMA_USE_LEGACY -fpic -g -O2 -Wall -pedantic -mtune=native -c RcppArmaHelper.cpp -o RcppArmaHelper.o
g++-14 -std=gnu++17 -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'/home/hornik/tmp/R.check/r-patched-gcc/Work/build/Packages/RcppArmadillo/include' -I/usr/local/include -D_FORTIFY_SOURCE=3 -fopenmp -DARMA_USE_LEGACY -fpic -g -O2 -Wall -pedantic -mtune=native -c RcppExports.cpp -o RcppExports.o
g++-14 -std=gnu++17 -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'/home/hornik/tmp/R.check/r-patched-gcc/Work/build/Packages/RcppArmadillo/include' -I/usr/local/include -D_FORTIFY_SOURCE=3 -fopenmp -DARMA_USE_LEGACY -fpic -g -O2 -Wall -pedantic -mtune=native -c SimpleAdjustComp.cpp -o SimpleAdjustComp.o
g++-14 -std=gnu++17 -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'/home/hornik/tmp/R.check/r-patched-gcc/Work/build/Packages/RcppArmadillo/include' -I/usr/local/include -D_FORTIFY_SOURCE=3 -fopenmp -DARMA_USE_LEGACY -fpic -g -O2 -Wall -pedantic -mtune=native -c TempCorrection.cpp -o TempCorrection.o
g++-14 -std=gnu++17 -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'/home/hornik/tmp/R.check/r-patched-gcc/Work/build/Packages/RcppArmadillo/include' -I/usr/local/include -D_FORTIFY_SOURCE=3 -fopenmp -DARMA_USE_LEGACY -fpic -g -O2 -Wall -pedantic -mtune=native -c UpdateFixedComps.cpp -o UpdateFixedComps.o
g++-14 -std=gnu++17 -shared -L/home/hornik/tmp/R.check/r-patched-gcc/Work/build/lib -Wl,-O1 -o BLMEngineInR.so AdjustForToxMode.o AdjustForWHAM.o CHESS.o CHESSIter.o CalcActivityCoef.o CalcChargeBalance.o CalcDonnanLayer.o CalcIonicStrength.o CalcIonicStrengthEffects.o CalcIterationTotalMoles.o CalcIterationTotals.o CalcResidAndError.o CalcSpecConc.o CalcStep.o CalcWHAMSpecCharge.o CompUpdate.o InitialGuess.o Jacobian.o MaxCompError.o RcppArmaHelper.o RcppExports.o SimpleAdjustComp.o TempCorrection.o UpdateFixedComps.o -fopenmp -llapack -L/home/hornik/tmp/R.check/r-patched-gcc/Work/build/lib -lRblas -lgfortran -lm -lquadmath -L/home/hornik/tmp/R.check/r-patched-gcc/Work/build/lib -lR
make[1]: Leaving directory '/home/hornik/tmp/scratch/RtmphIvizQ/R.INSTALL1418c037fb97a3/BLMEngineInR/src'
make[1]: Entering directory '/home/hornik/tmp/scratch/RtmphIvizQ/R.INSTALL1418c037fb97a3/BLMEngineInR/src'
make[1]: Leaving directory '/home/hornik/tmp/scratch/RtmphIvizQ/R.INSTALL1418c037fb97a3/BLMEngineInR/src'
installing to /home/hornik/tmp/R.check/r-patched-gcc/Work/build/Packages/00LOCK-BLMEngineInR/00new/BLMEngineInR/libs
** R
** data
*** moving datasets to lazyload DB
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
converting help for package ‘BLMEngineInR’
finding HTML links ... done
All_NIST20170203_reactions html
All_WATER23_reactions html
BLM html
BLMEngineInR-package html
BlankInputList html
BlankProblem html
BlankProblemList html
BlankWHAM html
CHESS html
CHESSLog html
CheckBLMObject html
CommonParameterDefinitions html
Components html
ConvertWHAMVThermoFile html
ConvertWindowsParamFile html
CriticalValues html
Cu_full_inorganic_problem html
Cu_full_organic_problem html
DefineProblem html
DefineWHAM html
GetData html
InLabs html
InVars html
ListCAT html
MW html
MassCompartments html
MatchInputsToProblem html
Ni_HCO3_full_organic_problem html
Ni_full_organic_problem html
Phases html
ProblemConversionFunctions html
ReadInputsFromFile html
SpecialDefs html
Species html
StoichConversionFunctions html
WriteDetailedFile html
WriteInputFile html
WriteParamFile html
WriteWHAMFile html
carbonate_system_problem html
water_MC_problem html
water_problem html
** building package indices
** 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 (BLMEngineInR)