* installing to library ‘/home/hornik/tmp/R.check/r-patched-gcc/Work/build/Packages’
* installing *source* package ‘landsepi’ ...
** package ‘landsepi’ successfully unpacked and MD5 sums checked
** using staged installation
configure: /home/hornik/tmp/R.check/r-patched-gcc/Work/build
checking whether to build debug version... no
checking whether to build profiling version... no
configure: /home/hornik/tmp/R.check/r-patched-gcc/Work/build
checking for Rcpp package... yes
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++17 accepts -g... yes
checking for cos in -lm... yes
checking for cblas_dgemm in -lgslcblas... yes
checking for gsl_blas_dgemm in -lgsl... yes
configure: creating ./config.status
config.status: creating src/Makevars
** libs
using C++ compiler: ‘g++-13 (Debian 13.2.0-23) 13.2.0’
make[1]: Entering directory '/tmp/RtmpcEVAn8/R.INSTALL1647f5548204b4/landsepi/src'
g++-13 -std=gnu++17 -I"/home/hornik/tmp/R.check/r-patched-gcc/Work/build/include" -DNDEBUG -I/usr/local/include -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/testthat/include' -I/usr/local/include -D_FORTIFY_SOURCE=3 -g -O2 -Wall -pedantic -mtune=native -fpic -g -O2 -Wall -pedantic -mtune=native -c Basic_patho.cpp -o Basic_patho.o
g++-13 -std=gnu++17 -I"/home/hornik/tmp/R.check/r-patched-gcc/Work/build/include" -DNDEBUG -I/usr/local/include -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/testthat/include' -I/usr/local/include -D_FORTIFY_SOURCE=3 -g -O2 -Wall -pedantic -mtune=native -fpic -g -O2 -Wall -pedantic -mtune=native -c Croptype.cpp -o Croptype.o
g++-13 -std=gnu++17 -I"/home/hornik/tmp/R.check/r-patched-gcc/Work/build/include" -DNDEBUG -I/usr/local/include -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/testthat/include' -I/usr/local/include -D_FORTIFY_SOURCE=3 -g -O2 -Wall -pedantic -mtune=native -fpic -g -O2 -Wall -pedantic -mtune=native -c Cultivar.cpp -o Cultivar.o
g++-13 -std=gnu++17 -I"/home/hornik/tmp/R.check/r-patched-gcc/Work/build/include" -DNDEBUG -I/usr/local/include -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/testthat/include' -I/usr/local/include -D_FORTIFY_SOURCE=3 -g -O2 -Wall -pedantic -mtune=native -fpic -g -O2 -Wall -pedantic -mtune=native -c Gene.cpp -o Gene.o
g++-13 -std=gnu++17 -I"/home/hornik/tmp/R.check/r-patched-gcc/Work/build/include" -DNDEBUG -I/usr/local/include -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/testthat/include' -I/usr/local/include -D_FORTIFY_SOURCE=3 -g -O2 -Wall -pedantic -mtune=native -fpic -g -O2 -Wall -pedantic -mtune=native -c Model.cpp -o Model.o
g++-13 -std=gnu++17 -I"/home/hornik/tmp/R.check/r-patched-gcc/Work/build/include" -DNDEBUG -I/usr/local/include -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/testthat/include' -I/usr/local/include -D_FORTIFY_SOURCE=3 -g -O2 -Wall -pedantic -mtune=native -fpic -g -O2 -Wall -pedantic -mtune=native -c RcppExports.cpp -o RcppExports.o
g++-13 -std=gnu++17 -I"/home/hornik/tmp/R.check/r-patched-gcc/Work/build/include" -DNDEBUG -I/usr/local/include -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/testthat/include' -I/usr/local/include -D_FORTIFY_SOURCE=3 -g -O2 -Wall -pedantic -mtune=native -fpic -g -O2 -Wall -pedantic -mtune=native -c Treatment.cpp -o Treatment.o
g++-13 -std=gnu++17 -I"/home/hornik/tmp/R.check/r-patched-gcc/Work/build/include" -DNDEBUG -I/usr/local/include -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/testthat/include' -I/usr/local/include -D_FORTIFY_SOURCE=3 -g -O2 -Wall -pedantic -mtune=native -fpic -g -O2 -Wall -pedantic -mtune=native -c functions.cpp -o functions.o
g++-13 -std=gnu++17 -I"/home/hornik/tmp/R.check/r-patched-gcc/Work/build/include" -DNDEBUG -I/usr/local/include -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/testthat/include' -I/usr/local/include -D_FORTIFY_SOURCE=3 -g -O2 -Wall -pedantic -mtune=native -fpic -g -O2 -Wall -pedantic -mtune=native -c gprof.cpp -o gprof.o
g++-13 -std=gnu++17 -I"/home/hornik/tmp/R.check/r-patched-gcc/Work/build/include" -DNDEBUG -I/usr/local/include -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/testthat/include' -I/usr/local/include -D_FORTIFY_SOURCE=3 -g -O2 -Wall -pedantic -mtune=native -fpic -g -O2 -Wall -pedantic -mtune=native -c initialisation.cpp -o initialisation.o
g++-13 -std=gnu++17 -I"/home/hornik/tmp/R.check/r-patched-gcc/Work/build/include" -DNDEBUG -I/usr/local/include -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/testthat/include' -I/usr/local/include -D_FORTIFY_SOURCE=3 -g -O2 -Wall -pedantic -mtune=native -fpic -g -O2 -Wall -pedantic -mtune=native -c printReadWrite.cpp -o printReadWrite.o
g++-13 -std=gnu++17 -shared -L/home/hornik/tmp/R.check/r-patched-gcc/Work/build/lib -Wl,-O1 -o landsepi.so Basic_patho.o Croptype.o Cultivar.o Gene.o Model.o RcppExports.o Treatment.o functions.o gprof.o initialisation.o printReadWrite.o -Wl,-O1 -lgsl -lgslcblas -lm -L/home/hornik/tmp/R.check/r-patched-gcc/Work/build/lib -lR
make[1]: Leaving directory '/tmp/RtmpcEVAn8/R.INSTALL1647f5548204b4/landsepi/src'
make[1]: Entering directory '/tmp/RtmpcEVAn8/R.INSTALL1647f5548204b4/landsepi/src'
make[1]: Leaving directory '/tmp/RtmpcEVAn8/R.INSTALL1647f5548204b4/landsepi/src'
installing to /home/hornik/tmp/R.check/r-patched-gcc/Work/build/Packages/00LOCK-landsepi/00new/landsepi/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 ‘landsepi’
finding HTML links ... done
AgriLand html
Cultivars_list html
LandsepiParams html
allocateCroptypeCultivars html
allocateCultivarGenes html
allocateLandscapeCroptypes html
antideriv_verhulst html
checkCroptypes html
checkCultivars html
checkCultivarsGenes html
checkDispersalHost html
checkDispersalPathogen html
checkGenes html
checkInoculum html
checkLandscape html
checkOutputs html
checkPI0_mat html
checkPathogen html
checkSimulParams html
checkTime html
checkTreatment html
compute_audpc100S html
createSimulParams html
demo_landsepi html
dispP html
epid_output html
evol_output html
getMatrixCroptypePatho html
getMatrixCultivarPatho html
getMatrixGenePatho html
getMatrixPolyPatho html
initialize-methods html
inoculumToMatrix html
invlogit html
is.in.01 html
is.positive html
is.strict.positive html
is.wholenumber html
landscapeTEST html
landsepi-package html
loadCroptypes html
loadCultivar html
loadDispersalHost html
loadDispersalPathogen html
loadGene html
loadInoculum html
loadLandscape html
loadOutputs html
loadPathogen html
loadSimulParams html
loadTreatment html
logit html
model_landsepi html
multiN html
periodic_cov html
plot_allocation html
plot_freqPatho html
plotland html
price_reduction html
print-methods html
resetCultivarsGenes html
runShinyApp html
runSimul html
saveDeploymentStrategy html
setCroptypes html
setCultivars html
setDispersalHost html
setDispersalPathogen html
setGenes html
setInoculum html
setLansdcape html
setOutputs html
setPathogen html
setSeed html
setSeedValue html
setTime html
setTreatment html
show-methods html
simul_landsepi html
summary-methods html
survivalProbToMatrix html
switch_patho_to_aggr html
updateReproSexProb html
updateSurvivalProb html
video 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 (landsepi)