* installing to library ‘/home/hornik/tmp/R.check/r-patched-gcc/Work/build/Packages’
* installing *source* package ‘SKAT’ ...
** package ‘SKAT’ successfully unpacked and MD5 sums checked
** using staged installation
** libs
using C++ compiler: ‘g++-13 (Debian 13.2.0-13) 13.2.0’
make[1]: Entering directory '/tmp/RtmpklIL2p/R.INSTALL2ead82315257aa/SKAT/src'
g++-13 -std=gnu++17 -I"/home/hornik/tmp/R.check/r-patched-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++-13 -std=gnu++17 -I"/home/hornik/tmp/R.check/r-patched-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++-13 -std=gnu++17 -I"/home/hornik/tmp/R.check/r-patched-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++-13 -std=gnu++17 -I"/home/hornik/tmp/R.check/r-patched-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++-13 -std=gnu++17 -I"/home/hornik/tmp/R.check/r-patched-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++-13 -std=gnu++17 -I"/home/hornik/tmp/R.check/r-patched-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++-13 -std=gnu++17 -I"/home/hornik/tmp/R.check/r-patched-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++-13 -std=gnu++17 -I"/home/hornik/tmp/R.check/r-patched-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++-13 -std=gnu++17 -I"/home/hornik/tmp/R.check/r-patched-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++-13 -std=gnu++17 -I"/home/hornik/tmp/R.check/r-patched-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++-13 -std=gnu++17 -I"/home/hornik/tmp/R.check/r-patched-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++-13 -std=gnu++17 -I"/home/hornik/tmp/R.check/r-patched-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++-13 -std=gnu++17 -I"/home/hornik/tmp/R.check/r-patched-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++-13 -std=gnu++17 -I"/home/hornik/tmp/R.check/r-patched-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++-13 -std=gnu++17 -shared -L/home/hornik/tmp/R.check/r-patched-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-patched-gcc/Work/build/lib -lR
make[1]: Leaving directory '/tmp/RtmpklIL2p/R.INSTALL2ead82315257aa/SKAT/src'
make[1]: Entering directory '/tmp/RtmpklIL2p/R.INSTALL2ead82315257aa/SKAT/src'
make[1]: Leaving directory '/tmp/RtmpklIL2p/R.INSTALL2ead82315257aa/SKAT/src'
installing to /home/hornik/tmp/R.check/r-patched-gcc/Work/build/Packages/00LOCK-SKAT/00new/SKAT/libs
** R
** data
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
converting help for package ‘SKAT’
finding HTML links ... done
Close_SSD html
Generate_SSD_SetID html
Get_ENT html
Get_Genotypes_SSD html
Get_Logistic_Weights html
Get_RequiredSampleSize html
Get_Resampling_Pvalue html
Open_SSD html
Power_Continuous html
Power_Logistic html
QQPlot_Adj html
Read_Plink_FAM html
Read_SNP_WeightFile html
Resampling_FWER html
SKAT.SSD.All html
SKAT.example.ChrX html
SKAT.example html
SKAT.fam.example html
SKAT.haplotypes html
SKAT html
SKATBinary.example html
SKATBinary html
SKATBinary_Robust html
SKATBinary_Single html
SKAT_ChrX html
SKAT_CommonRare html
SKAT_CommonRare_Robust html
SKAT_NULL_emmaX html
SKAT_Null_Model html
SKAT_Null_Model_MomentAdjust html
SSD_FILE_OPEN html
** 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)