* installing *source* package 'OmicFlow' ...
** package 'OmicFlow' successfully unpacked and MD5 sums checked
** using staged installation
** libs
using C++ compiler: 'g++.exe (GCC) 13.3.0'
make[1]: Entering directory '/d/temp/2025_11_12_01_50_01_6119/RtmpQXcPe1/R.INSTALL146686a8a56f8/OmicFlow/src'
g++ -std=gnu++17 -I"D:/RCompile/recent/R-4.4.3/include" -DNDEBUG -I'D:/RCompile/CRANpkg/lib/4.4/Rcpp/include' -I'D:/RCompile/CRANpkg/lib/4.4/RcppParallel/include' -I'D:/RCompile/CRANpkg/lib/4.4/RcppArmadillo/include' -I"d:/rtools44/x86_64-w64-mingw32.static.posix/include" -pedantic -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c RcppExports.cpp -o RcppExports.o
In file included from D:/RCompile/CRANpkg/lib/4.4/RcppArmadillo/include/current/armadillo:26,
from D:/RCompile/CRANpkg/lib/4.4/RcppArmadillo/include/RcppArmadillo/interface/RcppArmadilloForward.h:57,
from D:/RCompile/CRANpkg/lib/4.4/RcppArmadillo/include/RcppArmadillo.h:32,
from RcppExports.cpp:4:
D:/RCompile/CRANpkg/lib/4.4/RcppArmadillo/include/current/armadillo_bits/config.hpp:373:72: note: '#pragma message: NOTE: option ARMA_CRIPPLED_LAPACK is not supported'
373 | #pragma message ("NOTE: option ARMA_CRIPPLED_LAPACK is not supported")
| ^
g++ -std=gnu++17 -I"D:/RCompile/recent/R-4.4.3/include" -DNDEBUG -I'D:/RCompile/CRANpkg/lib/4.4/Rcpp/include' -I'D:/RCompile/CRANpkg/lib/4.4/RcppParallel/include' -I'D:/RCompile/CRANpkg/lib/4.4/RcppArmadillo/include' -I"d:/rtools44/x86_64-w64-mingw32.static.posix/include" -pedantic -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c branches.cpp -o branches.o
In file included from D:/RCompile/CRANpkg/lib/4.4/RcppArmadillo/include/current/armadillo:26,
from D:/RCompile/CRANpkg/lib/4.4/RcppArmadillo/include/RcppArmadillo/interface/RcppArmadilloForward.h:57,
from D:/RCompile/CRANpkg/lib/4.4/RcppArmadillo/include/RcppArmadillo.h:32,
from branches.h:4,
from branches.cpp:1:
D:/RCompile/CRANpkg/lib/4.4/RcppArmadillo/include/current/armadillo_bits/config.hpp:373:72: note: '#pragma message: NOTE: option ARMA_CRIPPLED_LAPACK is not supported'
373 | #pragma message ("NOTE: option ARMA_CRIPPLED_LAPACK is not supported")
| ^
g++ -std=gnu++17 -I"D:/RCompile/recent/R-4.4.3/include" -DNDEBUG -I'D:/RCompile/CRANpkg/lib/4.4/Rcpp/include' -I'D:/RCompile/CRANpkg/lib/4.4/RcppParallel/include' -I'D:/RCompile/CRANpkg/lib/4.4/RcppArmadillo/include' -I"d:/rtools44/x86_64-w64-mingw32.static.posix/include" -pedantic -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c distances.cpp -o distances.o
In file included from D:/RCompile/CRANpkg/lib/4.4/RcppArmadillo/include/current/armadillo:26,
from D:/RCompile/CRANpkg/lib/4.4/RcppArmadillo/include/RcppArmadillo/interface/RcppArmadilloForward.h:57,
from D:/RCompile/CRANpkg/lib/4.4/RcppArmadillo/include/RcppArmadillo.h:32,
from distances.h:4,
from distances.cpp:1:
D:/RCompile/CRANpkg/lib/4.4/RcppArmadillo/include/current/armadillo_bits/config.hpp:373:72: note: '#pragma message: NOTE: option ARMA_CRIPPLED_LAPACK is not supported'
373 | #pragma message ("NOTE: option ARMA_CRIPPLED_LAPACK is not supported")
| ^
In file included from D:/RCompile/CRANpkg/lib/4.4/RcppArmadillo/include/current/armadillo:860:
D:/RCompile/CRANpkg/lib/4.4/RcppArmadillo/include/current/armadillo_bits/spop_accu_meat.hpp: In instantiation of 'static typename T1::elem_type arma::spop_accu::apply(const arma::SpBase<typename T1::elem_type, T1>&) [with T1 = arma::SpGlue<arma::SpMat<double>, arma::SpMat<double>, arma::spglue_min>; typename T1::elem_type = double; typename T1::elem_type = double]':
D:/RCompile/CRANpkg/lib/4.4/RcppArmadillo/include/current/armadillo_bits/fn_accu.hpp:64:26: required from 'auto arma::accu(const T1&, const typename enable_if<is_arma_sparse_type<T1>::value>::result*) [with T1 = SpGlue<SpMat<double>, SpMat<double>, spglue_min>; typename enable_if<is_arma_sparse_type<T1>::value>::result = int]'
distances.cpp:32:28: required from here
D:/RCompile/CRANpkg/lib/4.4/RcppArmadillo/include/current/armadillo_bits/spop_accu_meat.hpp:47:74: warning: dereferencing type-punned pointer will break strict-aliasing rules [-Wstrict-aliasing]
47 | const SpSubview<eT>& sv = reinterpret_cast< const SpSubview<eT>& >(P.Q);
| ~~^
D:/RCompile/CRANpkg/lib/4.4/RcppArmadillo/include/current/armadillo_bits/spop_accu_meat.hpp: In instantiation of 'static typename T1::elem_type arma::spop_accu::apply(const arma::SpBase<typename T1::elem_type, T1>&) [with T1 = arma::SpGlue<arma::SpMat<double>, arma::SpMat<double>, arma::spglue_max>; typename T1::elem_type = double; typename T1::elem_type = double]':
D:/RCompile/CRANpkg/lib/4.4/RcppArmadillo/include/current/armadillo_bits/fn_accu.hpp:64:26: required from 'auto arma::accu(const T1&, const typename enable_if<is_arma_sparse_type<T1>::value>::result*) [with T1 = SpGlue<SpMat<double>, SpMat<double>, spglue_max>; typename enable_if<is_arma_sparse_type<T1>::value>::result = int]'
distances.cpp:33:30: required from here
D:/RCompile/CRANpkg/lib/4.4/RcppArmadillo/include/current/armadillo_bits/spop_accu_meat.hpp:47:74: warning: dereferencing type-punned pointer will break strict-aliasing rules [-Wstrict-aliasing]
g++ -std=gnu++17 -I"D:/RCompile/recent/R-4.4.3/include" -DNDEBUG -I'D:/RCompile/CRANpkg/lib/4.4/Rcpp/include' -I'D:/RCompile/CRANpkg/lib/4.4/RcppParallel/include' -I'D:/RCompile/CRANpkg/lib/4.4/RcppArmadillo/include' -I"d:/rtools44/x86_64-w64-mingw32.static.posix/include" -pedantic -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c interface.cpp -o interface.o
In file included from D:/RCompile/CRANpkg/lib/4.4/RcppArmadillo/include/current/armadillo:26,
from D:/RCompile/CRANpkg/lib/4.4/RcppArmadillo/include/RcppArmadillo/interface/RcppArmadilloForward.h:57,
from D:/RCompile/CRANpkg/lib/4.4/RcppArmadillo/include/RcppArmadillo.h:32,
from interface.cpp:1:
D:/RCompile/CRANpkg/lib/4.4/RcppArmadillo/include/current/armadillo_bits/config.hpp:373:72: note: '#pragma message: NOTE: option ARMA_CRIPPLED_LAPACK is not supported'
373 | #pragma message ("NOTE: option ARMA_CRIPPLED_LAPACK is not supported")
| ^
g++ -std=gnu++17 -shared -s -static-libgcc -o OmicFlow.dll tmp.def RcppExports.o branches.o distances.o interface.o -LD:/RCompile/CRANpkg/lib/4.4/RcppParallel/libs/x64 -lRcppParallel -LD:/RCompile/CRANpkg/lib/4.4/RcppParallel/lib/x64 -ltbb -ltbbmalloc -LD:/RCompile/recent/R-4.4.3/bin/x64 -lRlapack -LD:/RCompile/recent/R-4.4.3/bin/x64 -lRblas -lgfortran -lm -lquadmath -Ld:/rtools44/x86_64-w64-mingw32.static.posix/lib/x64 -Ld:/rtools44/x86_64-w64-mingw32.static.posix/lib -LD:/RCompile/recent/R-4.4.3/bin/x64 -lR
make[1]: Leaving directory '/d/temp/2025_11_12_01_50_01_6119/RtmpQXcPe1/R.INSTALL146686a8a56f8/OmicFlow/src'
make[1]: Entering directory '/d/temp/2025_11_12_01_50_01_6119/RtmpQXcPe1/R.INSTALL146686a8a56f8/OmicFlow/src'
make[1]: Leaving directory '/d/temp/2025_11_12_01_50_01_6119/RtmpQXcPe1/R.INSTALL146686a8a56f8/OmicFlow/src'
installing to d:/Rcompile/CRANpkg/lib/4.4/00LOCK-OmicFlow/00new/OmicFlow/libs/x64
** R
** exec
** inst
** 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
** testing if installed package can be loaded from final location
** testing if installed package keeps a record of temporary installation path
* MD5 sums
packaged installation of 'OmicFlow' as OmicFlow_1.4.0.zip
* DONE (OmicFlow)