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rcolgem log file (build_win64)
Wed May 25 15:32:12 2016: Building binary for package rcolgem (SVN revision 154)
using R version 3.3.0 Patched (2016-05-20 r70655) ...
* installing to library 'R:/lib/local/3.3'
* installing *source* package 'rcolgem' ...
** libs
*** arch - i386
c:/Rtools/mingw_32/bin/g++ -m32 -I"R:/lib/R/R-patched/include" -DNDEBUG -I"R:/lib/local/3.3/Rcpp/include" -I"R:/lib/local/3.3/RcppArmadillo/include" -I"R:/base/local215/include" -O2 -Wall -mtune=core2 -c RcppExports.cpp -o RcppExports.o
c:/Rtools/mingw_32/bin/g++ -m32 -I"R:/lib/R/R-patched/include" -DNDEBUG -I"R:/lib/local/3.3/Rcpp/include" -I"R:/lib/local/3.3/RcppArmadillo/include" -I"R:/base/local215/include" -O2 -Wall -mtune=core2 -c dAL0.cpp -o dAL0.o
dAL0.cpp: In function 'Rcpp::List dAL(double, Rcpp::NumericVector, Rcpp::List)':
dAL0.cpp:30:10: warning: unused variable 'z' [-Wunused-variable]
int k,l,z,w;
^
dAL0.cpp:30:12: warning: unused variable 'w' [-Wunused-variable]
int k,l,z,w;
^
c:/Rtools/mingw_32/bin/gcc -m32 -I"R:/lib/R/R-patched/include" -DNDEBUG -I"R:/lib/local/3.3/Rcpp/include" -I"R:/lib/local/3.3/RcppArmadillo/include" -I"R:/base/local215/include" -O3 -Wall -std=gnu99 -mtune=core2 -c dCA.c -o dCA.o
dCA.c: In function 'initfunc_dCA':
dCA.c:34:6: warning: variable 'Nparms' set but not used [-Wunused-but-set-variable]
int Nparms;
^
c:/Rtools/mingw_32/bin/gcc -m32 -I"R:/lib/R/R-patched/include" -DNDEBUG -I"R:/lib/local/3.3/Rcpp/include" -I"R:/lib/local/3.3/RcppArmadillo/include" -I"R:/base/local215/include" -O3 -Wall -std=gnu99 -mtune=core2 -c dQAL-6.3.c -o dQAL-6.3.o
dQAL-6.3.c: In function 'initfunc':
dQAL-6.3.c:32:6: warning: variable 'Nparms' set but not used [-Wunused-but-set-variable]
int Nparms;
^
dQAL-6.3.c: In function 'dQAL':
dQAL-6.3.c:56:12: warning: unused variable 'w' [-Wunused-variable]
int k,l,z,w;
^
dQAL-6.3.c: In function 'dQAL2012':
dQAL-6.3.c:132:12: warning: unused variable 'w' [-Wunused-variable]
int k,l,z,w;
^
c:/Rtools/mingw_32/bin/g++ -m32 -I"R:/lib/R/R-patched/include" -DNDEBUG -I"R:/lib/local/3.3/Rcpp/include" -I"R:/lib/local/3.3/RcppArmadillo/include" -I"R:/base/local215/include" -O2 -Wall -mtune=core2 -c phylo.source.attribution.cpp -o phylo.source.attribution.o
c:/Rtools/mingw_32/bin/g++ -m32 -I"R:/lib/R/R-patched/include" -DNDEBUG -I"R:/lib/local/3.3/Rcpp/include" -I"R:/lib/local/3.3/RcppArmadillo/include" -I"R:/base/local215/include" -O2 -Wall -mtune=core2 -c rcolgem_helpers.cpp -o rcolgem_helpers.o
rcolgem_helpers.cpp: In function 'Rcpp::NumericMatrix update_mstates(Rcpp::NumericVector, Rcpp::NumericMatrix, Rcpp::NumericMatrix)':
rcolgem_helpers.cpp:20:15: warning: unused variable 'z' [-Wunused-variable]
int u, k, l, z, w;
^
rcolgem_helpers.cpp:20:18: warning: unused variable 'w' [-Wunused-variable]
int u, k, l, z, w;
^
rcolgem_helpers.cpp: In function 'arma::mat update_mstates_arma(const uvec&, const mat&, arma::mat)':
rcolgem_helpers.cpp:46:20: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
for (int i = 0; i < extantLines.size(); i++){
^
rcolgem_helpers.cpp:45:6: warning: unused variable 'm' [-Wunused-variable]
int m = Q.n_rows;
^
rcolgem_helpers.cpp: In function 'arma::mat finite_size_correction(const vec&, const vec&, const uvec&, arma::mat)':
rcolgem_helpers.cpp:87:22: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
for (int iu = 0; iu < extantLines.size(); iu++){
^
c:/Rtools/mingw_32/bin/g++ -m32 -I"R:/lib/R/R-patched/include" -DNDEBUG -I"R:/lib/local/3.3/Rcpp/include" -I"R:/lib/local/3.3/RcppArmadillo/include" -I"R:/base/local215/include" -O2 -Wall -mtune=core2 -c treeSimulatorCpp2.cpp -o treeSimulatorCpp2.o
treeSimulatorCpp2.cpp: In function 'Rcpp::List simulateTreeCpp2(Rcpp::NumericVector, Rcpp::List, Rcpp::List, Rcpp::List, Rcpp::List, Rcpp::NumericVector, Rcpp::NumericVector, Rcpp::NumericMatrix, double, int, bool)':
treeSimulatorCpp2.cpp:129:18: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
for ( k = 0; k < Y.size(); k++)
^
treeSimulatorCpp2.cpp:131:20: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
for ( l = 0; l < Y.size(); l++){
^
treeSimulatorCpp2.cpp:222:10: warning: variable 'demes_found' set but not used [-Wunused-but-set-variable]
bool demes_found = false;
^
treeSimulatorCpp2.cpp:54:9: warning: unused variable 'maxHeight' [-Wunused-variable]
double maxHeight = maxSampleTime -tfin;
^
treeSimulatorCpp2.cpp:55:15: warning: unused variable 'deltat' [-Wunused-variable]
const double deltat = times[0] - times[1];
^
treeSimulatorCpp2.cpp:72:12: warning: unused variable 't0' [-Wunused-variable]
double t, t0, t1;
^
treeSimulatorCpp2.cpp:73:6: warning: unused variable 'internalNodeIndex' [-Wunused-variable]
int internalNodeIndex = n; // counter for internal branches
^
treeSimulatorCpp2.cpp:83:10: warning: unused variable 'ist' [-Wunused-variable]
int it, ist, k, l, nco, inco , i, stateOf_a, stateOf_recip;
^
treeSimulatorCpp2.cpp:83:21: warning: unused variable 'nco' [-Wunused-variable]
int it, ist, k, l, nco, inco , i, stateOf_a, stateOf_recip;
^
treeSimulatorCpp2.cpp:83:26: warning: unused variable 'inco' [-Wunused-variable]
int it, ist, k, l, nco, inco , i, stateOf_a, stateOf_recip;
^
treeSimulatorCpp2.cpp:83:36: warning: unused variable 'stateOf_a' [-Wunused-variable]
int it, ist, k, l, nco, inco , i, stateOf_a, stateOf_recip;
^
treeSimulatorCpp2.cpp:83:47: warning: unused variable 'stateOf_recip' [-Wunused-variable]
int it, ist, k, l, nco, inco , i, stateOf_a, stateOf_recip;
^
treeSimulatorCpp2.cpp:86:20: warning: unused variable 'cwk' [-Wunused-variable]
double r, rk, rl, cwk, cwl, twk, twl, h1;
^
treeSimulatorCpp2.cpp:86:25: warning: unused variable 'cwl' [-Wunused-variable]
double r, rk, rl, cwk, cwl, twk, twl, h1;
^
treeSimulatorCpp2.cpp:86:30: warning: unused variable 'twk' [-Wunused-variable]
double r, rk, rl, cwk, cwl, twk, twl, h1;
^
treeSimulatorCpp2.cpp:86:35: warning: unused variable 'twl' [-Wunused-variable]
double r, rk, rl, cwk, cwl, twk, twl, h1;
^
treeSimulatorCpp2.cpp:108:15: warning: unused variable 'deltah' [-Wunused-variable]
const double deltah = times[0] - times[1]; //note times decreasing
^
treeSimulatorCpp2.cpp:265:19: warning: 'u' may be used uninitialized in this function [-Wmaybe-uninitialized]
if ((i != u) && (extant[i]!=0)){
^
treeSimulatorCpp2.cpp:316:9: warning: 'l' may be used uninitialized in this function [-Wmaybe-uninitialized]
if (w!=l ){
^
c:/Rtools/mingw_32/bin/g++ -m32 -shared -s -static-libgcc -o rcolgem.dll tmp.def RcppExports.o dAL0.o dCA.o dQAL-6.3.o phylo.source.attribution.o rcolgem_helpers.o treeSimulatorCpp2.o -LR:/lib/R/R-patched/bin/i386 -lRlapack -LR:/lib/R/R-patched/bin/i386 -lRblas -lgfortran -lm -lquadmath -LR:/base/local215/lib/i386 -LR:/base/local215/lib -LR:/lib/R/R-patched/bin/i386 -lR
installing to R:/lib/local/3.3/rcolgem/libs/i386
*** arch - x64
c:/Rtools/mingw_64/bin/g++ -m64 -I"R:/lib/R/R-patched/include" -DNDEBUG -I"R:/lib/local/3.3/Rcpp/include" -I"R:/lib/local/3.3/RcppArmadillo/include" -I"R:/base/local215/include" -O2 -Wall -mtune=core2 -c RcppExports.cpp -o RcppExports.o
c:/Rtools/mingw_64/bin/g++ -m64 -I"R:/lib/R/R-patched/include" -DNDEBUG -I"R:/lib/local/3.3/Rcpp/include" -I"R:/lib/local/3.3/RcppArmadillo/include" -I"R:/base/local215/include" -O2 -Wall -mtune=core2 -c dAL0.cpp -o dAL0.o
dAL0.cpp: In function 'Rcpp::List dAL(double, Rcpp::NumericVector, Rcpp::List)':
dAL0.cpp:30:10: warning: unused variable 'z' [-Wunused-variable]
int k,l,z,w;
^
dAL0.cpp:30:12: warning: unused variable 'w' [-Wunused-variable]
int k,l,z,w;
^
c:/Rtools/mingw_64/bin/gcc -m64 -I"R:/lib/R/R-patched/include" -DNDEBUG -I"R:/lib/local/3.3/Rcpp/include" -I"R:/lib/local/3.3/RcppArmadillo/include" -I"R:/base/local215/include" -O2 -Wall -std=gnu99 -mtune=core2 -c dCA.c -o dCA.o
dCA.c: In function 'initfunc_dCA':
dCA.c:34:6: warning: variable 'Nparms' set but not used [-Wunused-but-set-variable]
int Nparms;
^
c:/Rtools/mingw_64/bin/gcc -m64 -I"R:/lib/R/R-patched/include" -DNDEBUG -I"R:/lib/local/3.3/Rcpp/include" -I"R:/lib/local/3.3/RcppArmadillo/include" -I"R:/base/local215/include" -O2 -Wall -std=gnu99 -mtune=core2 -c dQAL-6.3.c -o dQAL-6.3.o
dQAL-6.3.c: In function 'initfunc':
dQAL-6.3.c:32:6: warning: variable 'Nparms' set but not used [-Wunused-but-set-variable]
int Nparms;
^
dQAL-6.3.c: In function 'dQAL':
dQAL-6.3.c:56:12: warning: unused variable 'w' [-Wunused-variable]
int k,l,z,w;
^
dQAL-6.3.c: In function 'dQAL2012':
dQAL-6.3.c:132:12: warning: unused variable 'w' [-Wunused-variable]
int k,l,z,w;
^
c:/Rtools/mingw_64/bin/g++ -m64 -I"R:/lib/R/R-patched/include" -DNDEBUG -I"R:/lib/local/3.3/Rcpp/include" -I"R:/lib/local/3.3/RcppArmadillo/include" -I"R:/base/local215/include" -O2 -Wall -mtune=core2 -c phylo.source.attribution.cpp -o phylo.source.attribution.o
c:/Rtools/mingw_64/bin/g++ -m64 -I"R:/lib/R/R-patched/include" -DNDEBUG -I"R:/lib/local/3.3/Rcpp/include" -I"R:/lib/local/3.3/RcppArmadillo/include" -I"R:/base/local215/include" -O2 -Wall -mtune=core2 -c rcolgem_helpers.cpp -o rcolgem_helpers.o
rcolgem_helpers.cpp: In function 'Rcpp::NumericMatrix update_mstates(Rcpp::NumericVector, Rcpp::NumericMatrix, Rcpp::NumericMatrix)':
rcolgem_helpers.cpp:20:15: warning: unused variable 'z' [-Wunused-variable]
int u, k, l, z, w;
^
rcolgem_helpers.cpp:20:18: warning: unused variable 'w' [-Wunused-variable]
int u, k, l, z, w;
^
rcolgem_helpers.cpp: In function 'arma::mat update_mstates_arma(const uvec&, const mat&, arma::mat)':
rcolgem_helpers.cpp:46:20: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
for (int i = 0; i < extantLines.size(); i++){
^
rcolgem_helpers.cpp:45:6: warning: unused variable 'm' [-Wunused-variable]
int m = Q.n_rows;
^
rcolgem_helpers.cpp: In function 'arma::mat finite_size_correction(const vec&, const vec&, const uvec&, arma::mat)':
rcolgem_helpers.cpp:87:22: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
for (int iu = 0; iu < extantLines.size(); iu++){
^
c:/Rtools/mingw_64/bin/g++ -m64 -I"R:/lib/R/R-patched/include" -DNDEBUG -I"R:/lib/local/3.3/Rcpp/include" -I"R:/lib/local/3.3/RcppArmadillo/include" -I"R:/base/local215/include" -O2 -Wall -mtune=core2 -c treeSimulatorCpp2.cpp -o treeSimulatorCpp2.o
treeSimulatorCpp2.cpp: In function 'Rcpp::List simulateTreeCpp2(Rcpp::NumericVector, Rcpp::List, Rcpp::List, Rcpp::List, Rcpp::List, Rcpp::NumericVector, Rcpp::NumericVector, Rcpp::NumericMatrix, double, int, bool)':
treeSimulatorCpp2.cpp:129:18: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
for ( k = 0; k < Y.size(); k++)
^
treeSimulatorCpp2.cpp:131:20: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
for ( l = 0; l < Y.size(); l++){
^
treeSimulatorCpp2.cpp:222:10: warning: variable 'demes_found' set but not used [-Wunused-but-set-variable]
bool demes_found = false;
^
treeSimulatorCpp2.cpp:54:9: warning: unused variable 'maxHeight' [-Wunused-variable]
double maxHeight = maxSampleTime -tfin;
^
treeSimulatorCpp2.cpp:55:15: warning: unused variable 'deltat' [-Wunused-variable]
const double deltat = times[0] - times[1];
^
treeSimulatorCpp2.cpp:72:12: warning: unused variable 't0' [-Wunused-variable]
double t, t0, t1;
^
treeSimulatorCpp2.cpp:73:6: warning: unused variable 'internalNodeIndex' [-Wunused-variable]
int internalNodeIndex = n; // counter for internal branches
^
treeSimulatorCpp2.cpp:83:10: warning: unused variable 'ist' [-Wunused-variable]
int it, ist, k, l, nco, inco , i, stateOf_a, stateOf_recip;
^
treeSimulatorCpp2.cpp:83:21: warning: unused variable 'nco' [-Wunused-variable]
int it, ist, k, l, nco, inco , i, stateOf_a, stateOf_recip;
^
treeSimulatorCpp2.cpp:83:26: warning: unused variable 'inco' [-Wunused-variable]
int it, ist, k, l, nco, inco , i, stateOf_a, stateOf_recip;
^
treeSimulatorCpp2.cpp:83:36: warning: unused variable 'stateOf_a' [-Wunused-variable]
int it, ist, k, l, nco, inco , i, stateOf_a, stateOf_recip;
^
treeSimulatorCpp2.cpp:83:47: warning: unused variable 'stateOf_recip' [-Wunused-variable]
int it, ist, k, l, nco, inco , i, stateOf_a, stateOf_recip;
^
treeSimulatorCpp2.cpp:86:20: warning: unused variable 'cwk' [-Wunused-variable]
double r, rk, rl, cwk, cwl, twk, twl, h1;
^
treeSimulatorCpp2.cpp:86:25: warning: unused variable 'cwl' [-Wunused-variable]
double r, rk, rl, cwk, cwl, twk, twl, h1;
^
treeSimulatorCpp2.cpp:86:30: warning: unused variable 'twk' [-Wunused-variable]
double r, rk, rl, cwk, cwl, twk, twl, h1;
^
treeSimulatorCpp2.cpp:86:35: warning: unused variable 'twl' [-Wunused-variable]
double r, rk, rl, cwk, cwl, twk, twl, h1;
^
treeSimulatorCpp2.cpp:108:15: warning: unused variable 'deltah' [-Wunused-variable]
const double deltah = times[0] - times[1]; //note times decreasing
^
treeSimulatorCpp2.cpp:265:19: warning: 'u' may be used uninitialized in this function [-Wmaybe-uninitialized]
if ((i != u) && (extant[i]!=0)){
^
treeSimulatorCpp2.cpp:316:9: warning: 'l' may be used uninitialized in this function [-Wmaybe-uninitialized]
if (w!=l ){
^
c:/Rtools/mingw_64/bin/g++ -m64 -shared -s -static-libgcc -o rcolgem.dll tmp.def RcppExports.o dAL0.o dCA.o dQAL-6.3.o phylo.source.attribution.o rcolgem_helpers.o treeSimulatorCpp2.o -LR:/lib/R/R-patched/bin/x64 -lRlapack -LR:/lib/R/R-patched/bin/x64 -lRblas -lgfortran -lm -lquadmath -LR:/base/local215/lib/x64 -LR:/base/local215/lib -LR:/lib/R/R-patched/bin/x64 -lR
installing to R:/lib/local/3.3/rcolgem/libs/x64
** R
** inst
** preparing package for lazy loading
** help
Warning: R:/tmp/RtmpeOVxqw/R.INSTALLbb8483d603a/rcolgem/man/phylo.source.attribution.Rd:1: All text must be in a section
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded
*** arch - i386
*** arch - x64
* MD5 sums
packaged installation of 'rcolgem' as rcolgem_0.0.5.zip
* DONE (rcolgem)
Run time: 69.23 seconds.
