* installing *source* package ‘BayesReversePLLH’ ...
** package ‘BayesReversePLLH’ successfully unpacked and MD5 sums checked
** using staged installation
** libs
using C++ compiler: ‘clang version 18.1.2’
using C++11
make[1]: Entering directory '/data/gannet/ripley/R/packages/tests-clang/BayesReversePLLH/src'
/usr/local/clang18/bin/clang++ -std=gnu++11 -I"/data/gannet/ripley/R/R-clang/include" -DNDEBUG -I'/data/gannet/ripley/R/test-clang/Rcpp/include' -I'/data/gannet/ripley/R/test-clang/RcppArmadillo/include' -isystem /usr/local/clang18/include -I/usr/local/clang/include -fopenmp -fpic -O3 -Wall -pedantic -frtti -Wp,-D_FORTIFY_SOURCE=3 -c BayesReversePLLH.cpp -o BayesReversePLLH.o
In file included from BayesReversePLLH.cpp:5:
In file included from /data/gannet/ripley/R/test-clang/RcppArmadillo/include/RcppArmadillo.h:29:
In file included from /data/gannet/ripley/R/test-clang/RcppArmadillo/include/RcppArmadillo/interface/RcppArmadilloForward.h:57:
In file included from /data/gannet/ripley/R/test-clang/RcppArmadillo/include/armadillo:26:
/data/gannet/ripley/R/test-clang/RcppArmadillo/include/armadillo_bits/config.hpp:321:11: warning: INFO: support for ARMA_DONT_PRINT_ERRORS option has been removed [-W#pragma-messages]
321 | #pragma message ("INFO: support for ARMA_DONT_PRINT_ERRORS option has been removed")
| ^
/data/gannet/ripley/R/test-clang/RcppArmadillo/include/armadillo_bits/config.hpp:326:13: warning: INFO: suggest to use ARMA_WARN_LEVEL option instead [-W#pragma-messages]
326 | #pragma message ("INFO: suggest to use ARMA_WARN_LEVEL option instead")
| ^
/data/gannet/ripley/R/test-clang/RcppArmadillo/include/armadillo_bits/config.hpp:329:11: warning: INFO: see the documentation for details [-W#pragma-messages]
329 | #pragma message ("INFO: see the documentation for details")
| ^
BayesReversePLLH.cpp:345:10: warning: unused variable 'mean' [-Wunused-variable]
345 | double mean=0;
| ^~~~
BayesReversePLLH.cpp:513:10: warning: unused variable 'PSpike' [-Wunused-variable]
513 | double PSpike=PSlab/(1-PSlab);
| ^~~~~~
BayesReversePLLH.cpp:519:7: warning: unused variable 'b' [-Wunused-variable]
519 | int b=0;
| ^
BayesReversePLLH.cpp:520:7: warning: unused variable 'k' [-Wunused-variable]
520 | int k=0;
| ^
BayesReversePLLH.cpp:567:7: warning: unused variable 'which1' [-Wunused-variable]
567 | int which1=0;
| ^~~~~~
BayesReversePLLH.cpp:572:10: warning: unused variable 'mean2' [-Wunused-variable]
572 | double mean2=0;
| ^~~~~
BayesReversePLLH.cpp:578:10: warning: unused variable 'mean1' [-Wunused-variable]
578 | double mean1=0;
| ^~~~~
BayesReversePLLH.cpp:579:10: warning: unused variable 'Con' [-Wunused-variable]
579 | double Con=0;
| ^~~
BayesReversePLLH.cpp:638:10: warning: unused variable 'bprop' [-Wunused-variable]
638 | double bprop=1;
| ^~~~~
BayesReversePLLH.cpp:639:10: warning: unused variable 'Intb' [-Wunused-variable]
639 | double Intb=1;
| ^~~~
BayesReversePLLH.cpp:640:10: warning: unused variable 'Numb' [-Wunused-variable]
640 | double Numb=2;
| ^~~~
BayesReversePLLH.cpp:644:10: warning: unused variable 'prob1' [-Wunused-variable]
644 | double prob1=0;
| ^~~~~
BayesReversePLLH.cpp:645:10: warning: unused variable 'med2' [-Wunused-variable]
645 | double med2=0;
| ^~~~
BayesReversePLLH.cpp:1238:7: warning: unused variable 'b' [-Wunused-variable]
1238 | int b=0;
| ^
BayesReversePLLH.cpp:1246:10: warning: unused variable 'beta' [-Wunused-variable]
1246 | double beta = 1 ;
| ^~~~
BayesReversePLLH.cpp:1272:10: warning: unused variable 'betaprop' [-Wunused-variable]
1272 | double betaprop=0;
| ^~~~~~~~
BayesReversePLLH.cpp:1275:10: warning: unused variable 'svar' [-Wunused-variable]
1275 | double svar=1;
| ^~~~
BayesReversePLLH.cpp:1276:10: warning: unused variable 'Ints' [-Wunused-variable]
1276 | double Ints=1;
| ^~~~
BayesReversePLLH.cpp:1277:10: warning: unused variable 'Nums' [-Wunused-variable]
1277 | double Nums=2;
| ^~~~
BayesReversePLLH.cpp:1281:10: warning: unused variable 'mean1' [-Wunused-variable]
1281 | double mean1=0;
| ^~~~~
BayesReversePLLH.cpp:1282:10: warning: unused variable 'Con' [-Wunused-variable]
1282 | double Con=0;
| ^~~
BayesReversePLLH.cpp:1303:7: warning: unused variable 'which1' [-Wunused-variable]
1303 | int which1=0;
| ^~~~~~
BayesReversePLLH.cpp:1308:10: warning: unused variable 'bprop' [-Wunused-variable]
1308 | double bprop=1;
| ^~~~~
BayesReversePLLH.cpp:1309:10: warning: unused variable 'Intb' [-Wunused-variable]
1309 | double Intb=1;
| ^~~~
BayesReversePLLH.cpp:1310:10: warning: unused variable 'Numb' [-Wunused-variable]
1310 | double Numb=2;
| ^~~~
BayesReversePLLH.cpp:1314:10: warning: unused variable 'prob1' [-Wunused-variable]
1314 | double prob1=0;
| ^~~~~
BayesReversePLLH.cpp:1315:10: warning: unused variable 'med2' [-Wunused-variable]
1315 | double med2=0;
| ^~~~
BayesReversePLLH.cpp:1880:7: warning: unused variable 'b' [-Wunused-variable]
1880 | int b=0;
| ^
BayesReversePLLH.cpp:1881:7: warning: unused variable 'k' [-Wunused-variable]
1881 | int k=0;
| ^
BayesReversePLLH.cpp:1888:10: warning: unused variable 'beta' [-Wunused-variable]
1888 | double beta = 1 ;
| ^~~~
BayesReversePLLH.cpp:1914:10: warning: unused variable 'betaprop' [-Wunused-variable]
1914 | double betaprop=0;
| ^~~~~~~~
BayesReversePLLH.cpp:1917:10: warning: unused variable 'svar' [-Wunused-variable]
1917 | double svar=1;
| ^~~~
BayesReversePLLH.cpp:1918:10: warning: unused variable 'Ints' [-Wunused-variable]
1918 | double Ints=1;
| ^~~~
BayesReversePLLH.cpp:1919:10: warning: unused variable 'Nums' [-Wunused-variable]
1919 | double Nums=2;
| ^~~~
BayesReversePLLH.cpp:1921:10: warning: unused variable 'mean2' [-Wunused-variable]
1921 | double mean2=0;
| ^~~~~
BayesReversePLLH.cpp:1923:10: warning: unused variable 'mean1' [-Wunused-variable]
1923 | double mean1=0;
| ^~~~~
BayesReversePLLH.cpp:1924:10: warning: unused variable 'Con' [-Wunused-variable]
1924 | double Con=0;
| ^~~
BayesReversePLLH.cpp:1945:7: warning: unused variable 'which1' [-Wunused-variable]
1945 | int which1=0;
| ^~~~~~
BayesReversePLLH.cpp:1950:10: warning: unused variable 'bprop' [-Wunused-variable]
1950 | double bprop=1;
| ^~~~~
BayesReversePLLH.cpp:1951:10: warning: unused variable 'Intb' [-Wunused-variable]
1951 | double Intb=1;
| ^~~~
BayesReversePLLH.cpp:1952:10: warning: unused variable 'Numb' [-Wunused-variable]
1952 | double Numb=2;
| ^~~~
BayesReversePLLH.cpp:1956:10: warning: unused variable 'prob1' [-Wunused-variable]
1956 | double prob1=0;
| ^~~~~
BayesReversePLLH.cpp:1957:10: warning: unused variable 'med2' [-Wunused-variable]
1957 | double med2=0;
| ^~~~
BayesReversePLLH.cpp:2490:7: warning: unused variable 'b' [-Wunused-variable]
2490 | int b=0;
| ^
BayesReversePLLH.cpp:2491:7: warning: unused variable 'k' [-Wunused-variable]
2491 | int k=0;
| ^
BayesReversePLLH.cpp:2498:10: warning: unused variable 'beta' [-Wunused-variable]
2498 | double beta = 1 ;
| ^~~~
BayesReversePLLH.cpp:2524:10: warning: unused variable 'betaprop' [-Wunused-variable]
2524 | double betaprop=0;
| ^~~~~~~~
BayesReversePLLH.cpp:2527:10: warning: unused variable 'svar' [-Wunused-variable]
2527 | double svar=1;
| ^~~~
BayesReversePLLH.cpp:2528:10: warning: unused variable 'Ints' [-Wunused-variable]
2528 | double Ints=1;
| ^~~~
BayesReversePLLH.cpp:2529:10: warning: unused variable 'Nums' [-Wunused-variable]
2529 | double Nums=2;
| ^~~~
BayesReversePLLH.cpp:2531:10: warning: unused variable 'mean2' [-Wunused-variable]
2531 | double mean2=0;
| ^~~~~
BayesReversePLLH.cpp:2533:10: warning: unused variable 'mean1' [-Wunused-variable]
2533 | double mean1=0;
| ^~~~~
BayesReversePLLH.cpp:2534:10: warning: unused variable 'Con' [-Wunused-variable]
2534 | double Con=0;
| ^~~
BayesReversePLLH.cpp:2555:7: warning: unused variable 'which1' [-Wunused-variable]
2555 | int which1=0;
| ^~~~~~
BayesReversePLLH.cpp:2560:10: warning: unused variable 'bprop' [-Wunused-variable]
2560 | double bprop=1;
| ^~~~~
BayesReversePLLH.cpp:2561:10: warning: unused variable 'Intb' [-Wunused-variable]
2561 | double Intb=1;
| ^~~~
BayesReversePLLH.cpp:2562:10: warning: unused variable 'Numb' [-Wunused-variable]
2562 | double Numb=2;
| ^~~~
BayesReversePLLH.cpp:2566:10: warning: unused variable 'prob1' [-Wunused-variable]
2566 | double prob1=0;
| ^~~~~
BayesReversePLLH.cpp:2567:10: warning: unused variable 'med2' [-Wunused-variable]
2567 | double med2=0;
| ^~~~
BayesReversePLLH.cpp:3092:7: warning: unused variable 'b' [-Wunused-variable]
3092 | int b=0;
| ^
BayesReversePLLH.cpp:3100:10: warning: unused variable 'beta' [-Wunused-variable]
3100 | double beta = 1 ;
| ^~~~
BayesReversePLLH.cpp:3122:10: warning: unused variable 'betaprop' [-Wunused-variable]
3122 | double betaprop=0;
| ^~~~~~~~
BayesReversePLLH.cpp:3125:10: warning: unused variable 'svar' [-Wunused-variable]
3125 | double svar=1;
| ^~~~
BayesReversePLLH.cpp:3126:10: warning: unused variable 'Ints' [-Wunused-variable]
3126 | double Ints=1;
| ^~~~
BayesReversePLLH.cpp:3127:10: warning: unused variable 'Nums' [-Wunused-variable]
3127 | double Nums=2;
| ^~~~
BayesReversePLLH.cpp:3131:10: warning: unused variable 'mean1' [-Wunused-variable]
3131 | double mean1=0;
| ^~~~~
BayesReversePLLH.cpp:3132:10: warning: unused variable 'Con' [-Wunused-variable]
3132 | double Con=0;
| ^~~
BayesReversePLLH.cpp:3153:7: warning: unused variable 'which1' [-Wunused-variable]
3153 | int which1=0;
| ^~~~~~
BayesReversePLLH.cpp:3158:10: warning: unused variable 'bprop' [-Wunused-variable]
3158 | double bprop=1;
| ^~~~~
BayesReversePLLH.cpp:3159:10: warning: unused variable 'Intb' [-Wunused-variable]
3159 | double Intb=1;
| ^~~~
BayesReversePLLH.cpp:3160:10: warning: unused variable 'Numb' [-Wunused-variable]
3160 | double Numb=2;
| ^~~~
BayesReversePLLH.cpp:3164:10: warning: unused variable 'prob1' [-Wunused-variable]
3164 | double prob1=0;
| ^~~~~
BayesReversePLLH.cpp:3165:10: warning: unused variable 'med2' [-Wunused-variable]
3165 | double med2=0;
| ^~~~
BayesReversePLLH.cpp:3680:10: warning: unused variable 'PSpike' [-Wunused-variable]
3680 | double PSpike=PSlab/(1-PSlab);
| ^~~~~~
BayesReversePLLH.cpp:3686:7: warning: unused variable 'b' [-Wunused-variable]
3686 | int b=0;
| ^
BayesReversePLLH.cpp:3687:7: warning: unused variable 'k' [-Wunused-variable]
3687 | int k=0;
| ^
BayesReversePLLH.cpp:3727:7: warning: unused variable 'which1' [-Wunused-variable]
3727 | int which1=0;
| ^~~~~~
BayesReversePLLH.cpp:3732:10: warning: unused variable 'mean2' [-Wunused-variable]
3732 | double mean2=0;
| ^~~~~
BayesReversePLLH.cpp:3738:10: warning: unused variable 'mean1' [-Wunused-variable]
3738 | double mean1=0;
| ^~~~~
BayesReversePLLH.cpp:3739:10: warning: unused variable 'Con' [-Wunused-variable]
3739 | double Con=0;
| ^~~
BayesReversePLLH.cpp:3798:10: warning: unused variable 'bprop' [-Wunused-variable]
3798 | double bprop=1;
| ^~~~~
BayesReversePLLH.cpp:3799:10: warning: unused variable 'Intb' [-Wunused-variable]
3799 | double Intb=1;
| ^~~~
BayesReversePLLH.cpp:3800:10: warning: unused variable 'Numb' [-Wunused-variable]
3800 | double Numb=2;
| ^~~~
BayesReversePLLH.cpp:3804:10: warning: unused variable 'prob1' [-Wunused-variable]
3804 | double prob1=0;
| ^~~~~
BayesReversePLLH.cpp:3805:10: warning: unused variable 'med2' [-Wunused-variable]
3805 | double med2=0;
| ^~~~
88 warnings generated.
/usr/local/clang18/bin/clang++ -std=gnu++11 -I"/data/gannet/ripley/R/R-clang/include" -DNDEBUG -I'/data/gannet/ripley/R/test-clang/Rcpp/include' -I'/data/gannet/ripley/R/test-clang/RcppArmadillo/include' -isystem /usr/local/clang18/include -I/usr/local/clang/include -fopenmp -fpic -O3 -Wall -pedantic -frtti -Wp,-D_FORTIFY_SOURCE=3 -c RcppExports.cpp -o RcppExports.o
/usr/local/clang18/bin/clang++ -std=gnu++11 -shared -L/usr/local/clang/lib64 -L/usr/local/clang18/lib -L/usr/local/clang18/lib/x86_64-unknown-linux-gnu -L/usr/local/gcc13/lib64 -L/usr/local/lib64 -o BayesReversePLLH.so BayesReversePLLH.o RcppExports.o -fopenmp -L/data/gannet/ripley/R/R-clang/lib -lRlapack -L/data/gannet/ripley/R/R-clang/lib -lRblas -lFortran_main -lFortranRuntime -lFortranDecimal -lm
make[1]: Leaving directory '/data/gannet/ripley/R/packages/tests-clang/BayesReversePLLH/src'
make[1]: Entering directory '/data/gannet/ripley/R/packages/tests-clang/BayesReversePLLH/src'
make[1]: Leaving directory '/data/gannet/ripley/R/packages/tests-clang/BayesReversePLLH/src'
installing to /data/gannet/ripley/R/packages/tests-clang/BayesReversePLLH.Rcheck/00LOCK-BayesReversePLLH/00new/BayesReversePLLH/libs
** R
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
** building package indices
** 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 (BayesReversePLLH)