* installing to library ‘/home/hornik/tmp/R.check/r-patched-gcc/Work/build/Packages’
* installing *source* package ‘TreeSearch’ ...
** package ‘TreeSearch’ successfully unpacked and MD5 sums checked
** using staged installation
** libs
using C compiler: ‘gcc-13 (Debian 13.2.0-23) 13.2.0’
using C++ compiler: ‘g++-13 (Debian 13.2.0-23) 13.2.0’
using C++17
make[1]: Entering directory '/tmp/Rtmpfpa9dl/R.INSTALL14db0e233fc6ba/TreeSearch/src'
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'/home/hornik/tmp/R.check/r-patched-gcc/Work/build/Packages/TreeTools/include' -I/usr/local/include -D_FORTIFY_SOURCE=3 -fpic -g -O2 -Wall -Wstrict-prototypes -pedantic -mtune=native -c RMorphy.c -o RMorphy.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'/home/hornik/tmp/R.check/r-patched-gcc/Work/build/Packages/TreeTools/include' -I/usr/local/include -D_FORTIFY_SOURCE=3 -fpic -g -O2 -Wall -Wstrict-prototypes -pedantic -mtune=native -c RMorphyUtils.c -o RMorphyUtils.o
g++-13 -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/TreeTools/include' -I/usr/local/include -D_FORTIFY_SOURCE=3 -fpic -g -O2 -Wall -pedantic -mtune=native -c RcppExports.cpp -o RcppExports.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'/home/hornik/tmp/R.check/r-patched-gcc/Work/build/Packages/TreeTools/include' -I/usr/local/include -D_FORTIFY_SOURCE=3 -fpic -g -O2 -Wall -Wstrict-prototypes -pedantic -mtune=native -c TreeSearch-init.c -o TreeSearch-init.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'/home/hornik/tmp/R.check/r-patched-gcc/Work/build/Packages/TreeTools/include' -I/usr/local/include -D_FORTIFY_SOURCE=3 -fpic -g -O2 -Wall -Wstrict-prototypes -pedantic -mtune=native -c fitch.c -o fitch.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'/home/hornik/tmp/R.check/r-patched-gcc/Work/build/Packages/TreeTools/include' -I/usr/local/include -D_FORTIFY_SOURCE=3 -fpic -g -O2 -Wall -Wstrict-prototypes -pedantic -mtune=native -c morphy.c -o morphy.o
g++-13 -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/TreeTools/include' -I/usr/local/include -D_FORTIFY_SOURCE=3 -fpic -g -O2 -Wall -pedantic -mtune=native -c morphy_score.cpp -o morphy_score.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'/home/hornik/tmp/R.check/r-patched-gcc/Work/build/Packages/TreeTools/include' -I/usr/local/include -D_FORTIFY_SOURCE=3 -fpic -g -O2 -Wall -Wstrict-prototypes -pedantic -mtune=native -c mpl.c -o mpl.o
g++-13 -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/TreeTools/include' -I/usr/local/include -D_FORTIFY_SOURCE=3 -fpic -g -O2 -Wall -pedantic -mtune=native -c rearrange.cpp -o rearrange.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'/home/hornik/tmp/R.check/r-patched-gcc/Work/build/Packages/TreeTools/include' -I/usr/local/include -D_FORTIFY_SOURCE=3 -fpic -g -O2 -Wall -Wstrict-prototypes -pedantic -mtune=native -c statedata.c -o statedata.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'/home/hornik/tmp/R.check/r-patched-gcc/Work/build/Packages/TreeTools/include' -I/usr/local/include -D_FORTIFY_SOURCE=3 -fpic -g -O2 -Wall -Wstrict-prototypes -pedantic -mtune=native -c wagner.c -o wagner.o
g++-13 -std=gnu++17 -shared -L/home/hornik/tmp/R.check/r-patched-gcc/Work/build/lib -Wl,-O1 -o TreeSearch.so RMorphy.o RMorphyUtils.o RcppExports.o TreeSearch-init.o fitch.o morphy.o morphy_score.o mpl.o rearrange.o statedata.o wagner.o -L/home/hornik/tmp/R.check/r-patched-gcc/Work/build/lib -lR
make[1]: Leaving directory '/tmp/Rtmpfpa9dl/R.INSTALL14db0e233fc6ba/TreeSearch/src'
make[1]: Entering directory '/tmp/Rtmpfpa9dl/R.INSTALL14db0e233fc6ba/TreeSearch/src'
make[1]: Leaving directory '/tmp/Rtmpfpa9dl/R.INSTALL14db0e233fc6ba/TreeSearch/src'
installing to /home/hornik/tmp/R.check/r-patched-gcc/Work/build/Packages/00LOCK-TreeSearch/00new/TreeSearch/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 ‘TreeSearch’
finding HTML links ... done
AdditionTree html
finding level-2 HTML links ... done
AllSPR html
Carter1 html
CharacterLength html
ClusterStrings html
ConcordantInformation html
Consistency html
DoubleNNI html
GapHandler html
JackLabels html
Jackknife html
LengthAdded html
MaximizeParsimony html
MinimumLength html
MorphyErrorCheck html
MorphyTreeLength html
MorphyWeights html
NNI html
PhyDat2Morphy html
PlotCharacter html
PrepareDataProfile html
QuartetResolution html
RandomMorphyTree html
RandomTreeScore html
Ratchet html
RearrangeEdges html
SPR html
SingleCharMorphy html
SiteConcordance html
StepInformation html
StopUnlessBifurcating html
Suboptimality html
SuccessiveApproximations html
TBR html
TBRWarning html
TaxonInfluence html
TreeLength html
TreeSearch html
UnloadMorphy html
WhenFirstHit html
WithOneExtraStep html
cSPR html
congreveLamsdellMatrices html
dot-CombineResults html
dot-GapHandler html
dot-NonDuplicateRoot html
dot-UniqueExceptHits html
inapplicable.datasets html
is.morphyPtr html
mpl_apply_tipdata html
mpl_attach_rawdata html
mpl_attach_symbols html
mpl_delete_Morphy html
mpl_delete_rawdata html
mpl_first_down_recon html
mpl_first_up_recon html
mpl_get_charac_weight html
mpl_get_gaphandl html
mpl_get_num_charac html
mpl_get_num_internal_nodes html
mpl_get_numtaxa html
mpl_get_symbols html
mpl_init_Morphy html
mpl_new_Morphy html
mpl_second_down_recon html
mpl_second_up_recon html
mpl_set_charac_weight html
mpl_set_num_internal_nodes html
mpl_set_parsim_t html
mpl_translate_error html
mpl_update_lower_root html
mpl_update_tip html
profiles html
referenceTree html
summary.morphyPtr html
*** copying figures
** 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 (TreeSearch)