* installing *source* package ‘fastei’ ...
** this is package ‘fastei’ version ‘0.0.0.7’
** package ‘fastei’ successfully unpacked and MD5 sums checked
** using staged installation
** libs
using C compiler: ‘gcc (GCC) 15.1.1 20250521 (Red Hat 15.1.1-2)’
using C++ compiler: ‘g++ (GCC) 15.1.1 20250521 (Red Hat 15.1.1-2)’
make[1]: Entering directory '/data/gannet/ripley/R/packages/tests-devel/fastei/src'
g++ -std=gnu++17 -I"/data/gannet/ripley/R/R-devel/include" -DNDEBUG -I'/data/gannet/ripley/R/test-dev/Rcpp/include' -I/usr/local/include -fopenmp -fpic -g -O2 -Wall -pedantic -mtune=native -Wno-ignored-attributes -Wno-parentheses -Wp,-D_FORTIFY_SOURCE=3 -fexceptions -fstack-protector-strong -fstack-clash-protection -fcf-protection -c RcppExports.cpp -o RcppExports.o
gcc -I"/data/gannet/ripley/R/R-devel/include" -DNDEBUG -I'/data/gannet/ripley/R/test-dev/Rcpp/include' -I/usr/local/include -fpic -g -O2 -Wall -pedantic -mtune=native -Wp,-D_FORTIFY_SOURCE=3 -fexceptions -fstack-protector-strong -fstack-clash-protection -fcf-protection -Werror=implicit-function-declaration -Wstrict-prototypes -c bootstrap.c -o bootstrap.o
bootstrap.c: In function ‘bootstrapA’:
bootstrap.c:133:9: warning: unused variable ‘matsize’ [-Wunused-variable]
133 | int matsize = wmat->cols * xmat->rows;
| ^~~~~~~
bootstrap.c:132:9: warning: unused variable ‘samples’ [-Wunused-variable]
132 | int samples = bdim * bootiter;
| ^~~~~~~
bootstrap.c: In function ‘bootSingleMat’:
bootstrap.c:248:9: warning: unused variable ‘matsize’ [-Wunused-variable]
248 | int matsize = xmat->rows;
| ^~~~~~~
gcc -I"/data/gannet/ripley/R/R-devel/include" -DNDEBUG -I'/data/gannet/ripley/R/test-dev/Rcpp/include' -I/usr/local/include -fpic -g -O2 -Wall -pedantic -mtune=native -Wp,-D_FORTIFY_SOURCE=3 -fexceptions -fstack-protector-strong -fstack-clash-protection -fcf-protection -Werror=implicit-function-declaration -Wstrict-prototypes -c dynamic_program.c -o dynamic_program.o
dynamic_program.c: In function ‘aggregateGroups’:
dynamic_program.c:483:31: warning: ‘boundaries’ may be used uninitialized [-Wmaybe-uninitialized]
483 | bootstrapMatrix = testBootstrap(&quality, set_method, xmat, wmat, boundaries, -1, bootiter, q_method,
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
484 | p_method, convergence, log_convergence, maxIter, maxSeconds, *inputParams);
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
dynamic_program.c:446:10: note: ‘boundaries’ was declared here
446 | int *boundaries;
| ^~~~~~~~~~
gcc -I"/data/gannet/ripley/R/R-devel/include" -DNDEBUG -I'/data/gannet/ripley/R/test-dev/Rcpp/include' -I/usr/local/include -fpic -g -O2 -Wall -pedantic -mtune=native -Wp,-D_FORTIFY_SOURCE=3 -fexceptions -fstack-protector-strong -fstack-clash-protection -fcf-protection -Werror=implicit-function-declaration -Wstrict-prototypes -c exact.c -o exact.o
gcc -I"/data/gannet/ripley/R/R-devel/include" -DNDEBUG -I'/data/gannet/ripley/R/test-dev/Rcpp/include' -I/usr/local/include -fpic -g -O2 -Wall -pedantic -mtune=native -Wp,-D_FORTIFY_SOURCE=3 -fexceptions -fstack-protector-strong -fstack-clash-protection -fcf-protection -Werror=implicit-function-declaration -Wstrict-prototypes -c hitAndRun.c -o hitAndRun.o
hitAndRun.c: In function ‘generateOmegaSet’:
hitAndRun.c:212:14: warning: unused variable ‘arraySize’ [-Wunused-variable]
212 | uint32_t arraySize = M * S;
| ^~~~~~~~~
hitAndRun.c: In function ‘computeQ’:
hitAndRun.c:536:20: warning: unused variable ‘qsum’ [-Wunused-variable]
536 | double qsum = 0;
| ^~~~
hitAndRun.c: In function ‘computeQHitAndRun’:
hitAndRun.c:604:25: warning: unused variable ‘currentMatrix’ [-Wunused-variable]
604 | Matrix *currentMatrix = currentSet->data[s]; // Z
| ^~~~~~~~~~~~~
gcc -I"/data/gannet/ripley/R/R-devel/include" -DNDEBUG -I'/data/gannet/ripley/R/test-dev/Rcpp/include' -I/usr/local/include -fpic -g -O2 -Wall -pedantic -mtune=native -Wp,-D_FORTIFY_SOURCE=3 -fexceptions -fstack-protector-strong -fstack-clash-protection -fcf-protection -Werror=implicit-function-declaration -Wstrict-prototypes -c main.c -o main.o
main.c: In function ‘EMAlgoritm’:
main.c:520:20: warning: suggest parentheses around ‘&&’ within ‘||’ [-Wparentheses]
520 | if (i >= 1 && (fabs(newLL - oldLL) < LLconvergence || convergeMatrix(&newProbability, currentP, convergence)) ||
| ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
gcc -I"/data/gannet/ripley/R/R-devel/include" -DNDEBUG -I'/data/gannet/ripley/R/test-dev/Rcpp/include' -I/usr/local/include -fpic -g -O2 -Wall -pedantic -mtune=native -Wp,-D_FORTIFY_SOURCE=3 -fexceptions -fstack-protector-strong -fstack-clash-protection -fcf-protection -Werror=implicit-function-declaration -Wstrict-prototypes -c multinomial.c -o multinomial.o
gcc -I"/data/gannet/ripley/R/R-devel/include" -DNDEBUG -I'/data/gannet/ripley/R/test-dev/Rcpp/include' -I/usr/local/include -fpic -g -O2 -Wall -pedantic -mtune=native -Wp,-D_FORTIFY_SOURCE=3 -fexceptions -fstack-protector-strong -fstack-clash-protection -fcf-protection -Werror=implicit-function-declaration -Wstrict-prototypes -c multivariate-cdf.c -o multivariate-cdf.o
gcc -I"/data/gannet/ripley/R/R-devel/include" -DNDEBUG -I'/data/gannet/ripley/R/test-dev/Rcpp/include' -I/usr/local/include -fpic -g -O2 -Wall -pedantic -mtune=native -Wp,-D_FORTIFY_SOURCE=3 -fexceptions -fstack-protector-strong -fstack-clash-protection -fcf-protection -Werror=implicit-function-declaration -Wstrict-prototypes -c multivariate-pdf.c -o multivariate-pdf.o
gcc -I"/data/gannet/ripley/R/R-devel/include" -DNDEBUG -I'/data/gannet/ripley/R/test-dev/Rcpp/include' -I/usr/local/include -fpic -g -O2 -Wall -pedantic -mtune=native -Wp,-D_FORTIFY_SOURCE=3 -fexceptions -fstack-protector-strong -fstack-clash-protection -fcf-protection -Werror=implicit-function-declaration -Wstrict-prototypes -c utils_hash.c -o utils_hash.o
gcc -I"/data/gannet/ripley/R/R-devel/include" -DNDEBUG -I'/data/gannet/ripley/R/test-dev/Rcpp/include' -I/usr/local/include -fpic -g -O2 -Wall -pedantic -mtune=native -Wp,-D_FORTIFY_SOURCE=3 -fexceptions -fstack-protector-strong -fstack-clash-protection -fcf-protection -Werror=implicit-function-declaration -Wstrict-prototypes -c utils_matrix.c -o utils_matrix.o
utils_matrix.c:65:13: warning: ‘transposeMatrix’ defined but not used [-Wunused-function]
65 | static void transposeMatrix(const double *src, int rows, int cols, double *dst)
| ^~~~~~~~~~~~~~~
gcc -I"/data/gannet/ripley/R/R-devel/include" -DNDEBUG -I'/data/gannet/ripley/R/test-dev/Rcpp/include' -I/usr/local/include -fpic -g -O2 -Wall -pedantic -mtune=native -Wp,-D_FORTIFY_SOURCE=3 -fexceptions -fstack-protector-strong -fstack-clash-protection -fcf-protection -Werror=implicit-function-declaration -Wstrict-prototypes -c utils_multivariate.c -o utils_multivariate.o
utils_multivariate.c: In function ‘getAverageConditional’:
utils_multivariate.c:227:10: warning: unused variable ‘trans’ [-Wunused-variable]
227 | char trans = 'N'; // (There's no separate transpose flag in dger,
| ^~~~~
In file included from /data/gannet/ripley/R/R-devel/include/R.h:78,
from utils_multivariate.c:24:
utils_multivariate.c: In function ‘getMahanalobisDist’:
utils_multivariate.c:318:14: warning: ‘<unknown>’ may be used uninitialized [-Wmaybe-uninitialized]
318 | F77_CALL(dsymv)(&uplo, &n, &alpha, inverseSigma->data, &lda, diff, &incx, &beta, temp, &incy FCONE);
| ^
/data/gannet/ripley/R/R-devel/include/R_ext/RS.h:98:25: note: in definition of macro ‘F77_CALL’
98 | # define F77_CALL(x) x ## _
| ^
/data/gannet/ripley/R/R-devel/include/R_ext/BLAS.h:142:10: note: by argument 6 of type ‘const double *’ to ‘dsymv_’ declared here
142 | F77_NAME(dsymv)(const char *uplo, const BLAS_INT *n, const double *alpha,
| ^~~~~
/data/gannet/ripley/R/R-devel/include/R_ext/RS.h:98:25: note: in definition of macro ‘F77_CALL’
98 | # define F77_CALL(x) x ## _
| ^
/data/gannet/ripley/R/R-devel/include/R_ext/BLAS.h:142:1: note: in expansion of macro ‘F77_NAME’
142 | F77_NAME(dsymv)(const char *uplo, const BLAS_INT *n, const double *alpha,
| ^~~~~~~~
g++ -std=gnu++17 -I"/data/gannet/ripley/R/R-devel/include" -DNDEBUG -I'/data/gannet/ripley/R/test-dev/Rcpp/include' -I/usr/local/include -fopenmp -fpic -g -O2 -Wall -pedantic -mtune=native -Wno-ignored-attributes -Wno-parentheses -Wp,-D_FORTIFY_SOURCE=3 -fexceptions -fstack-protector-strong -fstack-clash-protection -fcf-protection -c wrapper.cpp -o wrapper.o
g++ -std=gnu++17 -shared -L/usr/local/lib64 -o fastei.so RcppExports.o bootstrap.o dynamic_program.o exact.o hitAndRun.o main.o multinomial.o multivariate-cdf.o multivariate-pdf.o utils_hash.o utils_matrix.o utils_multivariate.o wrapper.o -llapack -L/data/gannet/ripley/R/R-devel/lib -lRblas -lgfortran -lm -lquadmath -fopenmp
make[1]: Leaving directory '/data/gannet/ripley/R/packages/tests-devel/fastei/src'
make[1]: Entering directory '/data/gannet/ripley/R/packages/tests-devel/fastei/src'
make[1]: Leaving directory '/data/gannet/ripley/R/packages/tests-devel/fastei/src'
installing to /data/gannet/ripley/R/packages/tests-devel/fastei.Rcheck/00LOCK-fastei/00new/fastei/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 (fastei)