* installing to library ‘/home/hornik/tmp/R.check/r-release-gcc/Work/build/Packages’ * installing *source* package ‘SKAT’ ... ** package ‘SKAT’ successfully unpacked and MD5 sums checked ** using staged installation ** libs using C++ compiler: ‘g++-14 (Debian 14.2.0-6) 14.2.0’ make[1]: Entering directory '/home/hornik/tmp/scratch/RtmpnVy36Q/R.INSTALL28db5d494b72f4/SKAT/src' g++-14 -std=gnu++17 -I"/home/hornik/tmp/R.check/r-release-gcc/Work/build/include" -DNDEBUG -I/usr/local/include -D_FORTIFY_SOURCE=3 -fpic -g -O2 -Wall -pedantic -mtune=native -c Binary_ComputeExact.cpp -o Binary_ComputeExact.o Binary_ComputeExact.cpp: In member function ‘int ComputeExact::Run(int)’: Binary_ComputeExact.cpp:447:14: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector<double>::size_type’ {aka ‘long unsigned int’} [-Wsign-compare] 447 | for(l=0;l< m_Q.size(); l++){ | ~^~~~~~~~~~~~ Binary_ComputeExact.cpp: In member function ‘int ComputeExact::GetPvalues(double*, double*, double*, double*)’: Binary_ComputeExact.cpp:506:14: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector<double>::size_type’ {aka ‘long unsigned int’} [-Wsign-compare] 506 | for(i=0;i< m_pval.size(); i++){ | ~^~~~~~~~~~~~~~~ Binary_ComputeExact.cpp: In member function ‘int ComputeExact::PrintPval()’: Binary_ComputeExact.cpp:529:18: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector<double>::size_type’ {aka ‘long unsigned int’} [-Wsign-compare] 529 | for(int i=0;i< m_pval.size(); i++){ | ~^~~~~~~~~~~~~~~ g++-14 -std=gnu++17 -I"/home/hornik/tmp/R.check/r-release-gcc/Work/build/include" -DNDEBUG -I/usr/local/include -D_FORTIFY_SOURCE=3 -fpic -g -O2 -Wall -pedantic -mtune=native -c Binary_ComputeExactMC.cpp -o Binary_ComputeExactMC.o Binary_ComputeExactMC.cpp: In member function ‘int ComputeExactMC::Run()’: Binary_ComputeExactMC.cpp:388:22: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector<double>::size_type’ {aka ‘long unsigned int’} [-Wsign-compare] 388 | for(int l=0;l< m_Q.size(); l++){ | ~^~~~~~~~~~~~ Binary_ComputeExactMC.cpp: In member function ‘int ComputeExactMC::GetPvalues(double*, double*)’: Binary_ComputeExactMC.cpp:464:14: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector<double>::size_type’ {aka ‘long unsigned int’} [-Wsign-compare] 464 | for(i=0;i< m_pval.size(); i++){ | ~^~~~~~~~~~~~~~~ Binary_ComputeExactMC.cpp: In member function ‘int ComputeExactMC::PrintPvals()’: Binary_ComputeExactMC.cpp:478:18: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector<double>::size_type’ {aka ‘long unsigned int’} [-Wsign-compare] 478 | for(int i=0;i< m_pval.size(); i++){ | ~^~~~~~~~~~~~~~~ g++-14 -std=gnu++17 -I"/home/hornik/tmp/R.check/r-release-gcc/Work/build/include" -DNDEBUG -I/usr/local/include -D_FORTIFY_SOURCE=3 -fpic -g -O2 -Wall -pedantic -mtune=native -c Binary_ComputeExactSKATO.cpp -o Binary_ComputeExactSKATO.o Binary_ComputeExactSKATO.cpp: In member function ‘virtual double ComputeExactSKATO::CalTestStat(int, int*, bool, bool, int*)’: Binary_ComputeExactSKATO.cpp:82:15: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector<double>::size_type’ {aka ‘long unsigned int’} [-Wsign-compare] 82 | for(i=0; i<m_rcorr.size(); i++){ | ~^~~~~~~~~~~~~~~ Binary_ComputeExactSKATO.cpp: In member function ‘virtual double ComputeExactSKATO::CalTestStat_INV(int, int*, bool, bool, int*)’: Binary_ComputeExactSKATO.cpp:150:15: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector<double>::size_type’ {aka ‘long unsigned int’} [-Wsign-compare] 150 | for(i=0; i<m_rcorr.size(); i++){ | ~^~~~~~~~~~~~~~~ Binary_ComputeExactSKATO.cpp: In member function ‘virtual double ComputeExactSKATO::CalTestStat(int, int*, bool, bool, int*)’: Binary_ComputeExactSKATO.cpp:106:29: warning: ‘teststat’ may be used uninitialized [-Wmaybe-uninitialized] 106 | m_teststat[m_idx] = -teststat; | ^~~~~~~~~ Binary_ComputeExactSKATO.cpp:64:12: note: ‘teststat’ was declared here 64 | double teststat; | ^~~~~~~~ Binary_ComputeExactSKATO.cpp: In member function ‘virtual double ComputeExactSKATO::CalTestStat_INV(int, int*, bool, bool, int*)’: Binary_ComputeExactSKATO.cpp:168:29: warning: ‘teststat’ may be used uninitialized [-Wmaybe-uninitialized] 168 | m_teststat[m_idx] = -teststat; | ^~~~~~~~~ Binary_ComputeExactSKATO.cpp:133:12: note: ‘teststat’ was declared here 133 | double teststat; | ^~~~~~~~ g++-14 -std=gnu++17 -I"/home/hornik/tmp/R.check/r-release-gcc/Work/build/include" -DNDEBUG -I/usr/local/include -D_FORTIFY_SOURCE=3 -fpic -g -O2 -Wall -pedantic -mtune=native -c Binary_HyperGeo.cpp -o Binary_HyperGeo.o Binary_HyperGeo.cpp: In destructor ‘HyperGeo::~HyperGeo()’: Binary_HyperGeo.cpp:28:18: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector<double*>::size_type’ {aka ‘long unsigned int’} [-Wsign-compare] 28 | for(int i=0;i<m_probtbl.size();i++){ | ~^~~~~~~~~~~~~~~~~ g++-14 -std=gnu++17 -I"/home/hornik/tmp/R.check/r-release-gcc/Work/build/include" -DNDEBUG -I/usr/local/include -D_FORTIFY_SOURCE=3 -fpic -g -O2 -Wall -pedantic -mtune=native -c Binary_Permu_SKAT.cpp -o Binary_Permu_SKAT.o g++-14 -std=gnu++17 -I"/home/hornik/tmp/R.check/r-release-gcc/Work/build/include" -DNDEBUG -I/usr/local/include -D_FORTIFY_SOURCE=3 -fpic -g -O2 -Wall -pedantic -mtune=native -c Binary_global.cpp -o Binary_global.o g++-14 -std=gnu++17 -I"/home/hornik/tmp/R.check/r-release-gcc/Work/build/include" -DNDEBUG -I/usr/local/include -D_FORTIFY_SOURCE=3 -fpic -g -O2 -Wall -pedantic -mtune=native -c Binary_resampling.cpp -o Binary_resampling.o Binary_resampling.cpp: In function ‘void Test1(int*, int*, int*, double*, int*, int*, int*)’: Binary_resampling.cpp:196:22: warning: variable ‘ncase’ set but not used [-Wunused-but-set-variable] 196 | int i, n, m, ncase, idx; | ^~~~~ Binary_resampling.cpp:196:29: warning: variable ‘idx’ set but not used [-Wunused-but-set-variable] 196 | int i, n, m, ncase, idx; | ^~~ g++-14 -std=gnu++17 -I"/home/hornik/tmp/R.check/r-release-gcc/Work/build/include" -DNDEBUG -I/usr/local/include -D_FORTIFY_SOURCE=3 -fpic -g -O2 -Wall -pedantic -mtune=native -c bed_reader.cpp -o bed_reader.o bed_reader.cpp: In member function ‘void BedFileReader::read_One_SNP(int, int*, int*)’: bed_reader.cpp:274:16: warning: comparison of integer expressions of different signedness: ‘int’ and ‘size_t’ {aka ‘long unsigned int’} [-Wsign-compare] 274 | for(int i=0;i<this->m_line_counter; i++){ | ~^~~~~~~~~~~~~~~~~~~~~ bed_reader.cpp: In member function ‘void BedFileReader::decode_byte(int*, size_t*, int*, int*, size_t)’: bed_reader.cpp:623:13: warning: variable ‘flag’ set but not used [-Wunused-but-set-variable] 623 | int flag = 0; | ^~~~ g++-14 -std=gnu++17 -I"/home/hornik/tmp/R.check/r-release-gcc/Work/build/include" -DNDEBUG -I/usr/local/include -D_FORTIFY_SOURCE=3 -fpic -g -O2 -Wall -pedantic -mtune=native -c interface_new.cpp -o interface_new.o g++-14 -std=gnu++17 -I"/home/hornik/tmp/R.check/r-release-gcc/Work/build/include" -DNDEBUG -I/usr/local/include -D_FORTIFY_SOURCE=3 -fpic -g -O2 -Wall -pedantic -mtune=native -c interface_to_R.cpp -o interface_to_R.o g++-14 -std=gnu++17 -I"/home/hornik/tmp/R.check/r-release-gcc/Work/build/include" -DNDEBUG -I/usr/local/include -D_FORTIFY_SOURCE=3 -fpic -g -O2 -Wall -pedantic -mtune=native -c kernel_func.cpp -o kernel_func.o g++-14 -std=gnu++17 -I"/home/hornik/tmp/R.check/r-release-gcc/Work/build/include" -DNDEBUG -I/usr/local/include -D_FORTIFY_SOURCE=3 -fpic -g -O2 -Wall -pedantic -mtune=native -c mwo_reader.cpp -o mwo_reader.o mwo_reader.cpp: In constructor ‘MwoFileReader::MwoFileReader(char*, int*, char*)’: mwo_reader.cpp:100:31: warning: comparison of integer expressions of different signedness: ‘size_t’ {aka ‘long unsigned int’} and ‘int’ [-Wsign-compare] 100 | if ( this->m_win_size != -999 && this->m_ovlp_size != -999 ) | ~~~~~~~~~~~~~~~~~^~~~~~~ mwo_reader.cpp:100:60: warning: comparison of integer expressions of different signedness: ‘size_t’ {aka ‘long unsigned int’} and ‘int’ [-Wsign-compare] 100 | if ( this->m_win_size != -999 && this->m_ovlp_size != -999 ) | ~~~~~~~~~~~~~~~~~~^~~~~~~ mwo_reader.cpp: In member function ‘void MwoFileReader::upload_offsets_table()’: mwo_reader.cpp:175:38: warning: comparison of integer expressions of different signedness: ‘size_t’ {aka ‘long unsigned int’} and ‘int’ [-Wsign-compare] 175 | if( this->m_win_size != -999) | ~~~~~~~~~~~~~~~~~^~~~~~~ mwo_reader.cpp: In member function ‘void MwoFileReader::get_set(size_t, int*, size_t, int*, int, char*)’: mwo_reader.cpp:328:26: warning: comparison of integer expressions of different signedness: ‘size_t’ {aka ‘long unsigned int’} and ‘long int’ [-Wsign-compare] 328 | for (size_t i = 0; i < ss->m_snp.GetSize(); ++i){ | ~~^~~~~~~~~~~~~~~~~~~~~ mwo_reader.cpp:231:16: warning: variable ‘snp_id_ch_ind’ set but not used [-Wunused-but-set-variable] 231 | size_t snp_id_ch_ind = 0; | ^~~~~~~~~~~~~ mwo_reader.cpp: In member function ‘void MwoFileReader::get_set_new(size_t, int*, size_t, int*, int, char*, unsigned int*, int)’: mwo_reader.cpp:416:62: warning: comparison of integer expressions of different signedness: ‘size_t’ {aka ‘long unsigned int’} and ‘int’ [-Wsign-compare] 416 | if(buff[i] == '\n' || snp_ind==N_snp) // if first char in line == '\n' - next_snp_set will start at next char | ~~~~~~~^~~~~~~ mwo_reader.cpp:489:26: warning: comparison of integer expressions of different signedness: ‘size_t’ {aka ‘long unsigned int’} and ‘long int’ [-Wsign-compare] 489 | for (size_t i = 0; i < ss->m_snp.GetSize(); ++i){ | ~~^~~~~~~~~~~~~~~~~~~~~ mwo_reader.cpp:377:16: warning: variable ‘snp_id_ch_ind’ set but not used [-Wunused-but-set-variable] 377 | size_t snp_id_ch_ind = 0; | ^~~~~~~~~~~~~ mwo_reader.cpp: In member function ‘void MwoFileReader::prepare_out_array_print_snpset_to_file(snpset*, int, int*, size_t, int, int*, char*)’: mwo_reader.cpp:550:30: warning: comparison of integer expressions of different signedness: ‘size_t’ {aka ‘long unsigned int’} and ‘long int’ [-Wsign-compare] 550 | for (size_t i = 0; i < ss->m_snp.GetSize(); ++i) | ~~^~~~~~~~~~~~~~~~~~~~~ mwo_reader.cpp:564:38: warning: comparison of integer expressions of different signedness: ‘size_t’ {aka ‘long unsigned int’} and ‘long int’ [-Wsign-compare] 564 | for (size_t j = 0; j < ss->m_snp.GetAt(i)->m_char.GetSize(); ++j) | ~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ mwo_reader.cpp: In member function ‘void MwoFileReader::prepare_out_array_print_snpset_to_file_new(snpset*, int, int*, size_t, int, int*, char*)’: mwo_reader.cpp:653:30: warning: comparison of integer expressions of different signedness: ‘size_t’ {aka ‘long unsigned int’} and ‘long int’ [-Wsign-compare] 653 | for (size_t i = 0; i < ss->m_snp.GetSize(); ++i) | ~~^~~~~~~~~~~~~~~~~~~~~ mwo_reader.cpp:667:38: warning: comparison of integer expressions of different signedness: ‘size_t’ {aka ‘long unsigned int’} and ‘long int’ [-Wsign-compare] 667 | for (size_t j = 0; j < ss->m_snp.GetAt(i)->m_char.GetSize(); ++j) | ~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ mwo_reader.cpp: In member function ‘size_t MwoFileReader::get_NumberofSnps(int, int*)’: mwo_reader.cpp:772:28: warning: comparison of integer expressions of different signedness: ‘int’ and ‘size_t’ {aka ‘long unsigned int’} [-Wsign-compare] 772 | if (SetID > 0 && SetID < this->m_total_num_of_sets + 1){ | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ g++-14 -std=gnu++17 -I"/home/hornik/tmp/R.check/r-release-gcc/Work/build/include" -DNDEBUG -I/usr/local/include -D_FORTIFY_SOURCE=3 -fpic -g -O2 -Wall -pedantic -mtune=native -c qfc.cpp -o qfc.o g++-14 -std=gnu++17 -I"/home/hornik/tmp/R.check/r-release-gcc/Work/build/include" -DNDEBUG -I/usr/local/include -D_FORTIFY_SOURCE=3 -fpic -g -O2 -Wall -pedantic -mtune=native -c setid_bim_index.cpp -o setid_bim_index.o setid_bim_index.cpp: In destructor ‘Hasht::~Hasht()’: setid_bim_index.cpp:121:27: warning: comparison of integer expressions of different signedness: ‘int’ and ‘size_t’ {aka ‘long unsigned int’} [-Wsign-compare] 121 | for (int i = 0; i < m_num_of_snps_insetid; ++ i) | ~~^~~~~~~~~~~~~~~~~~~~~~~ g++-14 -std=gnu++17 -shared -L/home/hornik/tmp/R.check/r-release-gcc/Work/build/lib -Wl,-O1 -o SKAT.so Binary_ComputeExact.o Binary_ComputeExactMC.o Binary_ComputeExactSKATO.o Binary_HyperGeo.o Binary_Permu_SKAT.o Binary_global.o Binary_resampling.o bed_reader.o interface_new.o interface_to_R.o kernel_func.o mwo_reader.o qfc.o setid_bim_index.o -L/home/hornik/tmp/R.check/r-release-gcc/Work/build/lib -lR make[1]: Leaving directory '/home/hornik/tmp/scratch/RtmpnVy36Q/R.INSTALL28db5d494b72f4/SKAT/src' make[1]: Entering directory '/home/hornik/tmp/scratch/RtmpnVy36Q/R.INSTALL28db5d494b72f4/SKAT/src' make[1]: Leaving directory '/home/hornik/tmp/scratch/RtmpnVy36Q/R.INSTALL28db5d494b72f4/SKAT/src' installing to /home/hornik/tmp/R.check/r-release-gcc/Work/build/Packages/00LOCK-SKAT/00new/SKAT/libs ** R ** data ** 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 (SKAT)