* installing to library ‘/home/hornik/tmp/R.check/r-patched-gcc/Work/build/Packages’
* installing *source* package ‘TreeTools’ ...
** package ‘TreeTools’ successfully unpacked and MD5 sums checked
** using staged installation
** 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++17
make[1]: Entering directory '/tmp/RtmpSEAaY2/R.INSTALL303251675f57d7/TreeTools/src'
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/usr/local/include -D_FORTIFY_SOURCE=3 -fpic -g -O2 -Wall -pedantic -mtune=native -c ClusterTable.cpp -o ClusterTable.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/usr/local/include -D_FORTIFY_SOURCE=3 -fpic -g -O2 -Wall -pedantic -mtune=native -c RcppExports-manual.cpp -o RcppExports-manual.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/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/usr/local/include -D_FORTIFY_SOURCE=3 -fpic -g -O2 -Wall -Wstrict-prototypes -pedantic -mtune=native -c TreeTools-init.c -o TreeTools-init.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/usr/local/include -D_FORTIFY_SOURCE=3 -fpic -g -O2 -Wall -pedantic -mtune=native -c as_newick.cpp -o as_newick.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/usr/local/include -D_FORTIFY_SOURCE=3 -fpic -g -O2 -Wall -pedantic -mtune=native -c consensus.cpp -o consensus.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/usr/local/include -D_FORTIFY_SOURCE=3 -fpic -g -O2 -Wall -pedantic -mtune=native -c int_to_tree.cpp -o int_to_tree.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/usr/local/include -D_FORTIFY_SOURCE=3 -fpic -g -O2 -Wall -pedantic -mtune=native -c kept_vertices.cpp -o kept_vertices.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/usr/local/include -D_FORTIFY_SOURCE=3 -fpic -g -O2 -Wall -pedantic -mtune=native -c minimum_spanning_tree.cpp -o minimum_spanning_tree.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/usr/local/include -D_FORTIFY_SOURCE=3 -fpic -g -O2 -Wall -pedantic -mtune=native -c path_lengths.cpp -o path_lengths.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/usr/local/include -D_FORTIFY_SOURCE=3 -fpic -g -O2 -Wall -pedantic -mtune=native -c splits.cpp -o splits.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/usr/local/include -D_FORTIFY_SOURCE=3 -fpic -g -O2 -Wall -pedantic -mtune=native -c splits_to_tree.cpp -o splits_to_tree.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/usr/local/include -D_FORTIFY_SOURCE=3 -fpic -g -O2 -Wall -pedantic -mtune=native -c tips_in_splits.cpp -o tips_in_splits.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/usr/local/include -D_FORTIFY_SOURCE=3 -fpic -g -O2 -Wall -pedantic -mtune=native -c tree_shape.cpp -o tree_shape.o
g++-13 -std=gnu++17 -shared -L/home/hornik/tmp/R.check/r-patched-gcc/Work/build/lib -Wl,-O1 -o TreeTools.so ClusterTable.o RcppExports-manual.o RcppExports.o TreeTools-init.o as_newick.o consensus.o int_to_tree.o kept_vertices.o minimum_spanning_tree.o path_lengths.o splits.o splits_to_tree.o tips_in_splits.o tree_shape.o -L/home/hornik/tmp/R.check/r-patched-gcc/Work/build/lib -lR
make[1]: Leaving directory '/tmp/RtmpSEAaY2/R.INSTALL303251675f57d7/TreeTools/src'
make[1]: Entering directory '/tmp/RtmpSEAaY2/R.INSTALL303251675f57d7/TreeTools/src'
make[1]: Leaving directory '/tmp/RtmpSEAaY2/R.INSTALL303251675f57d7/TreeTools/src'
installing to /home/hornik/tmp/R.check/r-patched-gcc/Work/build/Packages/00LOCK-TreeTools/00new/TreeTools/libs
** R
** data
*** moving datasets to lazyload DB
** inst
** byte-compile and prepare package for lazy loading
Creating a generic function for ‘match’ from package ‘base’ in package ‘TreeTools’
Creating a generic function for ‘%in%’ from package ‘base’ in package ‘TreeTools’
** help
*** installing help indices
converting help for package ‘TreeTools’
finding HTML links ... done
AddTip html
finding level-2 HTML links ... done
AncestorEdge html
ApeTime html
ArtificialExtinction html
CharacterInformation html
CladeSizes html
CladisticInfo html
ClusterTable-methods html
ClusterTable html
CollapseNode html
CompatibleSplits html
Consensus html
ConsensusWithout html
ConstrainedNJ html
DescendantEdges html
DoubleFactorial html
DropTip html
EdgeAncestry html
EdgeDistances html
EndSentence html
EnforceOutgroup html
ExtractTaxa html
GenerateTree html
Hamming html
ImposeConstraint html
KeptPaths html
KeptVerts html
LabelSplits html
LeafLabelInterchange html
ListAncestors html
Lobo.data html
MRCA html
MSTEdges html
MakeTreeBinary html
MatrixToPhyDat html
MorphoBankDecode html
N1Spr html
NDescendants html
NJTree html
NPartitionPairs html
NRooted html
NSplits html
NTip html
NewickTree html
Neworder html
NodeDepth html
NodeOrder html
PairwiseDistances html
PathLengths html
PhyToString html
PolarizeSplits html
ReadCharacters html
ReadMrBayesTrees html
ReadTntTree html
Renumber html
RenumberTips html
Reorder html
RightmostCharacter html
RoguePlot html
RootNode html
RootTree html
SampleOne html
SortTree html
SpectrumLegend html
SplitFrequency html
SplitInformation html
SplitMatchProbability html
Splits html
SplitsInBinaryTree html
Stemwardness html
Subsplit html
Subtree html
SupportColour html
TipLabels html
TipTimedTree html
TipsInSplits html
TotalCopheneticIndex html
TreeIsRooted html
TreeNumber html
TreeShape html
TreeTools-package html
TreesMatchingSplit html
TreesMatchingTree html
TrivialSplits html
TrivialTree html
Unquote html
UnrootedTreesMatchingSplit html
UnshiftTree html
WriteTntCharacters html
as.Newick html
as.multiPhylo html
brewer html
dot-RandomParent html
doubleFactorials html
edge_to_splits html
is.TreeNumber html
logDoubleFactorials html
match.Splits html
nRootedShapes html
print.TreeNumber html
sapply64 html
sort.multiPhylo html
xor 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 (TreeTools)