* installing to library ‘/home/hornik/tmp/R.check/r-patched-gcc/Work/build/Packages’
* installing *source* package ‘cheddar’ ...
** package ‘cheddar’ successfully unpacked and MD5 sums checked
** using staged installation
** libs
using C++ compiler: ‘g++-13 (Debian 13.2.0-13) 13.2.0’
make[1]: Entering directory '/tmp/RtmpJiIsSp/R.INSTALL1fbfd52256aed4/cheddar/src'
g++-13 -std=gnu++17 -I"/home/hornik/tmp/R.check/r-patched-gcc/Work/build/include" -DNDEBUG -I/usr/local/include -D_FORTIFY_SOURCE=3 -fpic -g -O2 -Wall -pedantic -mtune=native -c anneal.cpp -o anneal.o
g++-13 -std=gnu++17 -I"/home/hornik/tmp/R.check/r-patched-gcc/Work/build/include" -DNDEBUG -I/usr/local/include -D_FORTIFY_SOURCE=3 -fpic -g -O2 -Wall -pedantic -mtune=native -c cheddar.cpp -o cheddar.o
g++-13 -std=gnu++17 -I"/home/hornik/tmp/R.check/r-patched-gcc/Work/build/include" -DNDEBUG -I/usr/local/include -D_FORTIFY_SOURCE=3 -fpic -g -O2 -Wall -pedantic -mtune=native -c shortest_paths.cpp -o shortest_paths.o
g++-13 -std=gnu++17 -I"/home/hornik/tmp/R.check/r-patched-gcc/Work/build/include" -DNDEBUG -I/usr/local/include -D_FORTIFY_SOURCE=3 -fpic -g -O2 -Wall -pedantic -mtune=native -c trophic_chains.cpp -o trophic_chains.o
trophic_chains.cpp: In instantiation of ‘void TrophicChains<Visitor>::visit(Visitor&) const [with Visitor = CollectChainLengthsVisitor]’:
trophic_chains.cpp:349:17: required from here
trophic_chains.cpp:92:22: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector<std::vector<int> >::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
92 | for(int n = 0; n < adjacency_.size(); ++n)
| ~~^~~~~~~~~~~~~~~~~~~
trophic_chains.cpp:128:25: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector<int>::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
128 | for(int j=0; j<adjacency_[m].size(); ++j)
| ~^~~~~~~~~~~~~~~~~~~~~
trophic_chains.cpp: In instantiation of ‘void TrophicChains<Visitor>::visit(Visitor&) const [with Visitor = PrintChainsVisitor]’:
trophic_chains.cpp:412:17: required from here
trophic_chains.cpp:92:22: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector<std::vector<int> >::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
92 | for(int n = 0; n < adjacency_.size(); ++n)
| ~~^~~~~~~~~~~~~~~~~~~
trophic_chains.cpp:128:25: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector<int>::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
128 | for(int j=0; j<adjacency_[m].size(); ++j)
| ~^~~~~~~~~~~~~~~~~~~~~
trophic_chains.cpp: In instantiation of ‘void TrophicChains<Visitor>::visit(Visitor&) const [with Visitor = CollectChainsVisitor]’:
trophic_chains.cpp:480:17: required from here
trophic_chains.cpp:92:22: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector<std::vector<int> >::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
92 | for(int n = 0; n < adjacency_.size(); ++n)
| ~~^~~~~~~~~~~~~~~~~~~
trophic_chains.cpp:128:25: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector<int>::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
128 | for(int j=0; j<adjacency_[m].size(); ++j)
| ~^~~~~~~~~~~~~~~~~~~~~
trophic_chains.cpp: In instantiation of ‘void TrophicChains<Visitor>::visit(Visitor&) const [with Visitor = ChainStatsVisitor]’:
trophic_chains.cpp:552:17: required from here
trophic_chains.cpp:92:22: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector<std::vector<int> >::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
92 | for(int n = 0; n < adjacency_.size(); ++n)
| ~~^~~~~~~~~~~~~~~~~~~
trophic_chains.cpp:128:25: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector<int>::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
128 | for(int j=0; j<adjacency_[m].size(); ++j)
| ~^~~~~~~~~~~~~~~~~~~~~
g++-13 -std=gnu++17 -shared -L/home/hornik/tmp/R.check/r-patched-gcc/Work/build/lib -Wl,-O1 -o cheddar.so anneal.o cheddar.o shortest_paths.o trophic_chains.o -L/home/hornik/tmp/R.check/r-patched-gcc/Work/build/lib -lR
make[1]: Leaving directory '/tmp/RtmpJiIsSp/R.INSTALL1fbfd52256aed4/cheddar/src'
make[1]: Entering directory '/tmp/RtmpJiIsSp/R.INSTALL1fbfd52256aed4/cheddar/src'
make[1]: Leaving directory '/tmp/RtmpJiIsSp/R.INSTALL1fbfd52256aed4/cheddar/src'
installing to /home/hornik/tmp/R.check/r-patched-gcc/Work/build/Packages/00LOCK-cheddar/00new/cheddar/libs
** R
** data
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
converting help for package ‘cheddar’
finding HTML links ... done
AggregateCommunities html
ApplyByClass html
Benguela html
BodyMassB html
BroadstoneStream html
CP html
CPS html
ChesapeakeBay html
CollectionApply html
CollectionCPS html
CollectionNPS html
CollectionTLPS html
Community html
CommunityCollection html
CommunityHas html
CommunityPropertyNames html
Degree html
DegreeDistribution html
Intervality html
IsCannibal html
LinearRegressionByClass html
LoadCollection html
LoadCommunity html
LumpNodes html
LumpTrophicSpecies html
Millstream html
NP html
NPS html
NodeConnectivity html
NodeMNUtilities html
NodeNameIndices html
NodePropertyNames html
NumberOfNodes html
NumberOfTrophicLinks html
NvMConvexHull html
NvMLinearRegressions html
NvMTriTrophicStatistics html
NvMTriTrophicTable html
Omnivory html
OrderCollection html
OrderCommunity html
PlotAuppervAlower html
PlotCircularWeb html
PlotHelpers html
PlotNPS html
PlotNPSDistribution html
PlotPyramid html
PlotRankNPS html
PlotSpectrum html
PlotTLPS html
PlotWagonWheel html
PlotWebByLevel html
PredationMatrix html
PredationMatrixToLinks html
QuantitativeDescriptors html
RemoveCannibalisticLinks html
RemoveIsolatedNodes html
RemoveNodes html
ResourceLargerThanConsumer html
ResourcesByNode html
ShortestPaths html
SiteBySpeciesMatrix html
SkipwithPond html
TL84 html
TLP html
TLPS html
ThreeNodeChains html
TrophicChains html
TrophicChainsStats html
TrophicLevels html
TrophicLinkPropertyNames html
TrophicSimilarity html
TrophicSpecies html
YthanEstuary html
cheddar html
pHWebs html
subset.CommunityCollection 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 (cheddar)