* installing to library ‘/home/hornik/tmp/R.check/r-patched-gcc/Work/build/Packages’
* installing *source* package ‘POUMM’ ...
** package ‘POUMM’ successfully unpacked and MD5 sums checked
** using staged installation
** libs
using C++ compiler: ‘g++-13 (Debian 13.2.0-13) 13.2.0’
using C++11
make[1]: Entering directory '/tmp/RtmpwkptxC/R.INSTALL34f8d17c52abfd/POUMM/src'
g++-13 -std=gnu++11 -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 Rcpp.cpp -o Rcpp.o
In file included from AbcPOUMM.h:28,
from Rcpp.cpp:28:
./SPLITT.h:2014: warning: ignoring ‘#pragma omp simd’ [-Wunknown-pragmas]
2014 | _PRAGMA_OMP_SIMD
|
./SPLITT.h:2032: warning: ignoring ‘#pragma omp simd’ [-Wunknown-pragmas]
2032 | _PRAGMA_OMP_SIMD
|
./SPLITT.h:2045: warning: ignoring ‘#pragma omp simd’ [-Wunknown-pragmas]
2045 | _PRAGMA_OMP_SIMD
|
./SPLITT.h:2057: warning: ignoring ‘#pragma omp simd’ [-Wunknown-pragmas]
2057 | _PRAGMA_OMP_SIMD
|
./SPLITT.h:2067: warning: ignoring ‘#pragma omp simd’ [-Wunknown-pragmas]
2067 | _PRAGMA_OMP_SIMD
|
./SPLITT.h:2093: warning: ignoring ‘#pragma omp parallel’ [-Wunknown-pragmas]
2093 | #pragma omp parallel
|
./SPLITT.h:2095: warning: ignoring ‘#pragma omp for’ [-Wunknown-pragmas]
2095 | _PRAGMA_OMP_FOR_SIMD
|
./SPLITT.h:2106: warning: ignoring ‘#pragma omp barrier’ [-Wunknown-pragmas]
2106 | #pragma omp barrier
|
./SPLITT.h:2109: warning: ignoring ‘#pragma omp for’ [-Wunknown-pragmas]
2109 | _PRAGMA_OMP_FOR_SIMD
|
./SPLITT.h:2120: warning: ignoring ‘#pragma omp barrier’ [-Wunknown-pragmas]
2120 | #pragma omp barrier
|
./SPLITT.h:2123: warning: ignoring ‘#pragma omp for’ [-Wunknown-pragmas]
2123 | _PRAGMA_OMP_FOR_SIMD
|
./SPLITT.h:2139: warning: ignoring ‘#pragma omp parallel’ [-Wunknown-pragmas]
2139 | #pragma omp parallel
|
./SPLITT.h:2148: warning: ignoring ‘#pragma omp for’ [-Wunknown-pragmas]
2148 | _PRAGMA_OMP_FOR_SIMD
|
./SPLITT.h:2158: warning: ignoring ‘#pragma omp for’ [-Wunknown-pragmas]
2158 | _PRAGMA_OMP_FOR_SIMD
|
./SPLITT.h:2184: warning: ignoring ‘#pragma omp parallel’ [-Wunknown-pragmas]
2184 | #pragma omp parallel
|
./SPLITT.h:2224: warning: ignoring ‘#pragma omp parallel’ [-Wunknown-pragmas]
2224 | #pragma omp parallel
|
./SPLITT.h:2226: warning: ignoring ‘#pragma omp for’ [-Wunknown-pragmas]
2226 | _PRAGMA_OMP_FOR_SIMD
|
./SPLITT.h:2237: warning: ignoring ‘#pragma omp for’ [-Wunknown-pragmas]
2237 | _PRAGMA_OMP_FOR_SIMD
|
./SPLITT.h:2251: warning: ignoring ‘#pragma omp parallel’ [-Wunknown-pragmas]
2251 | #pragma omp parallel
|
./SPLITT.h:2253: warning: ignoring ‘#pragma omp for’ [-Wunknown-pragmas]
2253 | _PRAGMA_OMP_FOR_SIMD
|
./SPLITT.h:2261: warning: ignoring ‘#pragma omp for’ [-Wunknown-pragmas]
2261 | _PRAGMA_OMP_FOR_SIMD
|
./SPLITT.h:2272: warning: ignoring ‘#pragma omp parallel’ [-Wunknown-pragmas]
2272 | #pragma omp parallel
|
./SPLITT.h:2281: warning: ignoring ‘#pragma omp for’ [-Wunknown-pragmas]
2281 | _PRAGMA_OMP_FOR_SIMD
|
./SPLITT.h:2292: warning: ignoring ‘#pragma omp barrier’ [-Wunknown-pragmas]
2292 | #pragma omp barrier
|
./SPLITT.h:2295: warning: ignoring ‘#pragma omp for’ [-Wunknown-pragmas]
2295 | _PRAGMA_OMP_FOR_SIMD
|
./SPLITT.h:2304: warning: ignoring ‘#pragma omp simd’ [-Wunknown-pragmas]
2304 | _PRAGMA_OMP_SIMD
|
./SPLITT.h:2318: warning: ignoring ‘#pragma omp simd’ [-Wunknown-pragmas]
2318 | _PRAGMA_OMP_SIMD
|
./SPLITT.h:2336: warning: ignoring ‘#pragma omp parallel’ [-Wunknown-pragmas]
2336 | #pragma omp parallel
|
./SPLITT.h:2345: warning: ignoring ‘#pragma omp for’ [-Wunknown-pragmas]
2345 | _PRAGMA_OMP_FOR_SIMD
|
./SPLITT.h:2356: warning: ignoring ‘#pragma omp barrier’ [-Wunknown-pragmas]
2356 | #pragma omp barrier
|
./SPLITT.h:2359: warning: ignoring ‘#pragma omp for’ [-Wunknown-pragmas]
2359 | _PRAGMA_OMP_FOR_SIMD
|
./SPLITT.h:2369: warning: ignoring ‘#pragma omp simd’ [-Wunknown-pragmas]
2369 | _PRAGMA_OMP_SIMD
|
./SPLITT.h:2384: warning: ignoring ‘#pragma omp parallel’ [-Wunknown-pragmas]
2384 | #pragma omp parallel
|
./SPLITT.h:2393: warning: ignoring ‘#pragma omp for’ [-Wunknown-pragmas]
2393 | _PRAGMA_OMP_FOR_SIMD
|
./SPLITT.h:2403: warning: ignoring ‘#pragma omp barrier’ [-Wunknown-pragmas]
2403 | #pragma omp barrier
|
./SPLITT.h:2406: warning: ignoring ‘#pragma omp for’ [-Wunknown-pragmas]
2406 | _PRAGMA_OMP_FOR_SIMD
|
./SPLITT.h:2424: warning: ignoring ‘#pragma omp simd’ [-Wunknown-pragmas]
2424 | _PRAGMA_OMP_SIMD
|
./SPLITT.h:2568: warning: ignoring ‘#pragma omp simd’ [-Wunknown-pragmas]
2568 | _PRAGMA_OMP_SIMD
|
./SPLITT.h:2582: warning: ignoring ‘#pragma omp simd’ [-Wunknown-pragmas]
2582 | _PRAGMA_OMP_SIMD
|
./SPLITT.h:2591: warning: ignoring ‘#pragma omp simd’ [-Wunknown-pragmas]
2591 | _PRAGMA_OMP_SIMD
|
./SPLITT.h:2599: warning: ignoring ‘#pragma omp parallel’ [-Wunknown-pragmas]
2599 | #pragma omp parallel
|
./SPLITT.h:2608: warning: ignoring ‘#pragma omp for’ [-Wunknown-pragmas]
2608 | _PRAGMA_OMP_FOR_SIMD
|
./SPLITT.h:2617: warning: ignoring ‘#pragma omp for’ [-Wunknown-pragmas]
2617 | _PRAGMA_OMP_FOR_SIMD
|
./SPLITT.h: In instantiation of ‘void SPLITT::PostOrderTraversal<TraversalSpecification>::TraverseTreeMultiThreadLoopVisits() [with TraversalSpecification = SPLITT::AbcPOUMM<SPLITT::OrderedTree<unsigned int, double> >]’:
./SPLITT.h:1891:46: required from ‘void SPLITT::PostOrderTraversal<TraversalSpecification>::TraverseTree(ModeType) [with TraversalSpecification = SPLITT::AbcPOUMM<SPLITT::OrderedTree<unsigned int, double> >; ModeType = SPLITT::PostOrderMode]’
./SPLITT.h:585:28: required from ‘SPLITT::TraversalTask<TraversalSpecification>::StateType SPLITT::TraversalTask<TraversalSpecification>::TraverseTree(const ParameterType&, SPLITT::uint) [with TraversalSpecification = SPLITT::AbcPOUMM<SPLITT::OrderedTree<unsigned int, double> >; StateType = std::vector<double>; ParameterType = std::vector<double>; SPLITT::uint = unsigned int]’
Rcpp.cpp:111:51: required from here
./SPLITT.h:2141:8: warning: variable ‘tid’ set but not used [-Wunused-but-set-variable]
2141 | uint tid;
| ^~~
g++-13 -std=gnu++11 -shared -L/home/hornik/tmp/R.check/r-patched-gcc/Work/build/lib -Wl,-O1 -o POUMM.so Rcpp.o -L/home/hornik/tmp/R.check/r-patched-gcc/Work/build/lib -lR
make[1]: Leaving directory '/tmp/RtmpwkptxC/R.INSTALL34f8d17c52abfd/POUMM/src'
make[1]: Entering directory '/tmp/RtmpwkptxC/R.INSTALL34f8d17c52abfd/POUMM/src'
make[1]: Leaving directory '/tmp/RtmpwkptxC/R.INSTALL34f8d17c52abfd/POUMM/src'
installing to /home/hornik/tmp/R.check/r-patched-gcc/Work/build/Packages/00LOCK-POUMM/00new/POUMM/libs
** R
** data
*** moving datasets to lazyload DB
** inst
** preparing package for lazy loading
** help
*** installing help indices
converting help for package ‘POUMM’
finding HTML links ... done
H2 html
OU html
POUMM html
POUMMIsADevRelease html
PhylogeneticH2 html
analyseMCMCs html
chld html
coef.POUMM html
covFunPOUMM html
covHPDFunPOUMM html
covPOUMM html
covVTipsGivenTreePOUMM html
dVNodesGivenTreePOUMM html
edgesFrom html
fitted.POUMM html
gPOUMM html
likPOUMMGivenTreeVTips html
likPOUMMGivenTreeVTipsC html
logLik.POUMM html
loglik_abc_g0_g0Prior html
maxLikPOUMMGivenTreeVTips html
mcmcPOUMMGivenPriorTreeVTips html
nobs.POUMM html
nodeTimes html
plot.POUMM html
plot.summary.POUMM html
pruneTree html
rTrajectoryOU html
rTrajectoryOUDef html
rVNodesGivenTreePOUMM html
residuals.POUMM html
simulatePOUMMLikelihoodMainLoop html
simulateTrait html
specPOUMM html
statistics html
summary.POUMM html
validateSpecPOUMM html
validateZTree html
vignetteCachedResults 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 (POUMM)