* installing *source* package ‘localScore’ ...
** this is package ‘localScore’ version ‘2.0.3’
** package ‘localScore’ successfully unpacked and MD5 sums checked
** using staged installation
** libs
using C++ compiler: ‘clang version 20.1.6’
make[1]: Entering directory '/data/gannet/ripley/R/packages/tests-clang/localScore/src'
clang++-20 -std=gnu++17 -I"/data/gannet/ripley/R/R-clang/include" -DNDEBUG -I'/data/gannet/ripley/R/test-clang/Rcpp/include' -isystem /usr/local/clang20/include -I/usr/local/clang/include -fpic -O3 -Wall -pedantic -frtti -Wp,-D_FORTIFY_SOURCE=3 -Wno-missing-template-arg-list-after-template-kw -c RcppExports.cpp -o RcppExports.o
clang++-20 -std=gnu++17 -I"/data/gannet/ripley/R/R-clang/include" -DNDEBUG -I'/data/gannet/ripley/R/test-clang/Rcpp/include' -isystem /usr/local/clang20/include -I/usr/local/clang/include -fpic -O3 -Wall -pedantic -frtti -Wp,-D_FORTIFY_SOURCE=3 -Wno-missing-template-arg-list-after-template-kw -c function_wrapper.cpp -o function_wrapper.o
clang++-20 -std=gnu++17 -I"/data/gannet/ripley/R/R-clang/include" -DNDEBUG -I'/data/gannet/ripley/R/test-clang/Rcpp/include' -isystem /usr/local/clang20/include -I/usr/local/clang/include -fpic -O3 -Wall -pedantic -frtti -Wp,-D_FORTIFY_SOURCE=3 -Wno-missing-template-arg-list-after-template-kw -c localScoreC.cpp -o localScoreC.o
function_wrapper.cpp:175:8: warning: unused variable 'checkOK' [-Wunused-variable]
175 | bool checkOK = checkKDMparameters(local_score, sequence_length, score_probabilities, sequence_min_, sequence_max_, score_values_) ;
| ^~~~~~~
function_wrapper.cpp:239:5: warning: misleading indentation; statement is not part of the previous 'if' [-Wmisleading-indentation]
239 | double p = calcul_karlin(local_score, as<std::vector<double>>(score_probabilities), as<int>(sequence_max_), -as<int>(sequence_min_), (long)sequence_length);
| ^
function_wrapper.cpp:236:3: note: previous statement is here
236 | if(esp>=0.0)
| ^
function_wrapper.cpp:228:8: warning: unused variable 'checkOK' [-Wunused-variable]
228 | bool checkOK = checkKDMparameters(local_score, sequence_length, score_probabilities, sequence_min_, sequence_max_, score_values_) ;
| ^~~~~~~
function_wrapper.cpp:262:8: warning: unused variable 'checkOK' [-Wunused-variable]
262 | bool checkOK = checkKDMparameters(1, 1, score_probabilities, sequence_min_, sequence_max_, score_values_) ;
| ^~~~~~~
function_wrapper.cpp:328:8: warning: unused variable 'checkOK' [-Wunused-variable]
328 | bool checkOK = checkKDMparameters(local_score, sequence_length, score_probabilities, sequence_min_, sequence_max_, score_values_) ;
| ^~~~~~~
function_wrapper.cpp:389:6: warning: misleading indentation; statement is not part of the previous 'if' [-Wmisleading-indentation]
389 | double p = calcul_probMaxPartialSum(k, as<std::vector<double>>(score_probabilities), max_score, -min_score);
| ^
function_wrapper.cpp:386:3: note: previous statement is here
386 | if(k<0)
| ^
function_wrapper.cpp:376:8: warning: unused variable 'checkOK' [-Wunused-variable]
376 | bool checkOK = checkKDMparameters(1, 1, score_probabilities, sequence_min_, sequence_max_, score_values_) ;
| ^~~~~~~
localScoreC.cpp:93:7: warning: unused variable 'fixNoScoreMatrixSize' [-Wunused-variable]
93 | int fixNoScoreMatrixSize = (numberOfLocalScores==0) ? 1 : 0; // needed to create finalScores Matrix in case of no localScore found
| ^~~~~~~~~~~~~~~~~~~~
7 warnings generated.
1 warning generated.
clang++-20 -std=gnu++17 -I"/data/gannet/ripley/R/R-clang/include" -DNDEBUG -I'/data/gannet/ripley/R/test-clang/Rcpp/include' -isystem /usr/local/clang20/include -I/usr/local/clang/include -fpic -O3 -Wall -pedantic -frtti -Wp,-D_FORTIFY_SOURCE=3 -Wno-missing-template-arg-list-after-template-kw -c pValueMethods.cpp -o pValueMethods.o
pValueMethods.cpp:512:16: warning: unused variable 'i' [-Wunused-variable]
512 | unsigned int i ;
| ^
pValueMethods.cpp:629:10: warning: unused variable 'K_plus' [-Wunused-variable]
629 | double K_plus = karlin_parameters[1] ;
| ^~~~~~
pValueMethods.cpp:713:10: warning: unused variable 'R' [-Wunused-variable]
713 | double R = roots_separated.mod_smaller_one[0].real();
| ^
3 warnings generated.
clang++-20 -std=gnu++17 -shared -L/usr/local/clang/lib64 -L/usr/local/clang20/lib -L/usr/local/clang20/lib/x86_64-unknown-linux-gnu -L/usr/local/lib64 -L/usr/local/clang20/lib/clang/20/lib/x86_64-unknown-linux-gnu -o localScore.so RcppExports.o function_wrapper.o localScoreC.o pValueMethods.o
make[1]: Leaving directory '/data/gannet/ripley/R/packages/tests-clang/localScore/src'
make[1]: Entering directory '/data/gannet/ripley/R/packages/tests-clang/localScore/src'
make[1]: Leaving directory '/data/gannet/ripley/R/packages/tests-clang/localScore/src'
installing to /data/gannet/ripley/R/packages/tests-clang/localScore.Rcheck/00LOCK-localScore/00new/localScore/libs
** R
** data
*** moving datasets to lazyload DB
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
** 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 (localScore)