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More on package install #1

Closed
Landau1994 opened this issue May 12, 2020 · 7 comments
Closed

More on package install #1

Landau1994 opened this issue May 12, 2020 · 7 comments

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@Landau1994
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Install this package in an environment in which provides a higher version of gcc(I choss gcc 5.0) can avoid some compile problem during package install.
@PaulingLiu
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Owner

We sincerely thank you for your kind reminder.

@zhoux85
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zhoux85 commented May 13, 2020 •
edited

Installing it on windows is not successful:
C:/rtools40/mingw32/bin/g++ -std=gnu++11 -shared -s -static-libgcc -o scibet.dll tmp.def RcppExports.o SciBet.o -LC:/PROGRA1/R/R-401.0/bin/i386 -lR
C:/rtools40/mingw32/bin/../lib/gcc/i686-w64-mingw32/8.3.0/../../../../i686-w64-mingw32/bin/ld.exe: SciBet.o:SciBet.cpp:(.text+0x18): undefined reference to omp_get_num_threads' C:/rtools40/mingw32/bin/../lib/gcc/i686-w64-mingw32/8.3.0/../../../../i686-w64-mingw32/bin/ld.exe: SciBet.o:SciBet.cpp:(.text+0x23): undefined reference to omp_get_thread_num'
C:/rtools40/mingw32/bin/../lib/gcc/i686-w64-mingw32/8.3.0/../../../../i686-w64-mingw32/bin/ld.exe: SciBet.o:SciBet.cpp:(.text+0x258): undefined reference to omp_get_num_threads' C:/rtools40/mingw32/bin/../lib/gcc/i686-w64-mingw32/8.3.0/../../../../i686-w64-mingw32/bin/ld.exe: SciBet.o:SciBet.cpp:(.text+0x263): undefined reference to omp_get_thread_num'
C:/rtools40/mingw32/bin/../lib/gcc/i686-w64-mingw32/8.3.0/../../../../i686-w64-mingw32/bin/ld.exe: SciBet.o:SciBet.cpp:(.text+0x356): undefined reference to omp_get_num_threads' C:/rtools40/mingw32/bin/../lib/gcc/i686-w64-mingw32/8.3.0/../../../../i686-w64-mingw32/bin/ld.exe: SciBet.o:SciBet.cpp:(.text+0x35d): undefined reference to omp_get_thread_num'
C:/rtools40/mingw32/bin/../lib/gcc/i686-w64-mingw32/8.3.0/../../../../i686-w64-mingw32/bin/ld.exe: SciBet.o:SciBet.cpp:(.text+0x478): undefined reference to omp_get_num_threads' C:/rtools40/mingw32/bin/../lib/gcc/i686-w64-mingw32/8.3.0/../../../../i686-w64-mingw32/bin/ld.exe: SciBet.o:SciBet.cpp:(.text+0x483): undefined reference to omp_get_thread_num'
C:/rtools40/mingw32/bin/../lib/gcc/i686-w64-mingw32/8.3.0/../../../../i686-w64-mingw32/bin/ld.exe: SciBet.o:SciBet.cpp:(.text+0x5e8): undefined reference to omp_get_num_threads' C:/rtools40/mingw32/bin/../lib/gcc/i686-w64-mingw32/8.3.0/../../../../i686-w64-mingw32/bin/ld.exe: SciBet.o:SciBet.cpp:(.text+0x5f3): undefined reference to omp_get_thread_num'
C:/rtools40/mingw32/bin/../lib/gcc/i686-w64-mingw32/8.3.0/../../../../i686-w64-mingw32/bin/ld.exe: SciBet.o:SciBet.cpp:(.text+0x808): undefined reference to omp_get_num_threads' C:/rtools40/mingw32/bin/../lib/gcc/i686-w64-mingw32/8.3.0/../../../../i686-w64-mingw32/bin/ld.exe: SciBet.o:SciBet.cpp:(.text+0x813): undefined reference to omp_get_thread_num'
C:/rtools40/mingw32/bin/../lib/gcc/i686-w64-mingw32/8.3.0/../../../../i686-w64-mingw32/bin/ld.exe: SciBet.o:SciBet.cpp:(.text+0x9ad): undefined reference to omp_get_num_threads' C:/rtools40/mingw32/bin/../lib/gcc/i686-w64-mingw32/8.3.0/../../../../i686-w64-mingw32/bin/ld.exe: SciBet.o:SciBet.cpp:(.text+0x9b4): undefined reference to omp_get_thread_num'
C:/rtools40/mingw32/bin/../lib/gcc/i686-w64-mingw32/8.3.0/../../../../i686-w64-mingw32/bin/ld.exe: SciBet.o:SciBet.cpp:(.text+0xf30): undefined reference to GOMP_parallel' C:/rtools40/mingw32/bin/../lib/gcc/i686-w64-mingw32/8.3.0/../../../../i686-w64-mingw32/bin/ld.exe: SciBet.o:SciBet.cpp:(.text+0x101f): undefined reference to GOMP_parallel'
C:/rtools40/mingw32/bin/../lib/gcc/i686-w64-mingw32/8.3.0/../../../../i686-w64-mingw32/bin/ld.exe: SciBet.o:SciBet.cpp:(.text+0x13b5): undefined reference to omp_set_num_threads' C:/rtools40/mingw32/bin/../lib/gcc/i686-w64-mingw32/8.3.0/../../../../i686-w64-mingw32/bin/ld.exe: SciBet.o:SciBet.cpp:(.text+0x1808): undefined reference to omp_get_num_threads'
C:/rtools40/mingw32/bin/../lib/gcc/i686-w64-mingw32/8.3.0/../../../../i686-w64-mingw32/bin/ld.exe: SciBet.o:SciBet.cpp:(.text+0x180f): undefined reference to omp_get_thread_num' C:/rtools40/mingw32/bin/../lib/gcc/i686-w64-mingw32/8.3.0/../../../../i686-w64-mingw32/bin/ld.exe: SciBet.o:SciBet.cpp:(.text+0x1d6c): undefined reference to GOMP_parallel'
C:/rtools40/mingw32/bin/../lib/gcc/i686-w64-mingw32/8.3.0/../../../../i686-w64-mingw32/bin/ld.exe: SciBet.o:SciBet.cpp:(.text+0x23fd): undefined reference to omp_set_num_threads' C:/rtools40/mingw32/bin/../lib/gcc/i686-w64-mingw32/8.3.0/../../../../i686-w64-mingw32/bin/ld.exe: SciBet.o:SciBet.cpp:(.text+0x267f): undefined reference to GOMP_parallel'
C:/rtools40/mingw32/bin/../lib/gcc/i686-w64-mingw32/8.3.0/../../../../i686-w64-mingw32/bin/ld.exe: SciBet.o:SciBet.cpp:(.text+0x29fe): undefined reference to omp_get_thread_num' C:/rtools40/mingw32/bin/../lib/gcc/i686-w64-mingw32/8.3.0/../../../../i686-w64-mingw32/bin/ld.exe: SciBet.o:SciBet.cpp:(.text+0x2a05): undefined reference to omp_get_num_threads'
C:/rtools40/mingw32/bin/../lib/gcc/i686-w64-mingw32/8.3.0/../../../../i686-w64-mingw32/bin/ld.exe: SciBet.o:SciBet.cpp:(.text+0x2e64): undefined reference to GOMP_parallel' C:/rtools40/mingw32/bin/../lib/gcc/i686-w64-mingw32/8.3.0/../../../../i686-w64-mingw32/bin/ld.exe: SciBet.o:SciBet.cpp:(.text+0x2f49): undefined reference to omp_set_num_threads'
C:/rtools40/mingw32/bin/../lib/gcc/i686-w64-mingw32/8.3.0/../../../../i686-w64-mingw32/bin/ld.exe: SciBet.o:SciBet.cpp:(.text+0x3a00): undefined reference to GOMP_parallel' C:/rtools40/mingw32/bin/../lib/gcc/i686-w64-mingw32/8.3.0/../../../../i686-w64-mingw32/bin/ld.exe: SciBet.o:SciBet.cpp:(.text+0x3aa7): undefined reference to omp_set_num_threads'
C:/rtools40/mingw32/bin/../lib/gcc/i686-w64-mingw32/8.3.0/../../../../i686-w64-mingw32/bin/ld.exe: SciBet.o:SciBet.cpp:(.text+0x40f3): undefined reference to GOMP_parallel' C:/rtools40/mingw32/bin/../lib/gcc/i686-w64-mingw32/8.3.0/../../../../i686-w64-mingw32/bin/ld.exe: SciBet.o:SciBet.cpp:(.text+0x42be): undefined reference to GOMP_parallel'
C:/rtools40/mingw32/bin/../lib/gcc/i686-w64-mingw32/8.3.0/../../../../i686-w64-mingw32/bin/ld.exe: SciBet.o:SciBet.cpp:(.text+0x4504): undefined reference to omp_set_num_threads' C:/rtools40/mingw32/bin/../lib/gcc/i686-w64-mingw32/8.3.0/../../../../i686-w64-mingw32/bin/ld.exe: SciBet.o:SciBet.cpp:(.text+0x45e0): undefined reference to GOMP_parallel'
C:/rtools40/mingw32/bin/../lib/gcc/i686-w64-mingw32/8.3.0/../../../../i686-w64-mingw32/bin/ld.exe: SciBet.o:SciBet.cpp:(.text$_ZN5Eigen8internal29general_matrix_matrix_productIidLi0ELb0EdLi0ELb0ELi0EE3runEiiiPKdiS4_iPdidRNS0_15level3_blockingIddEEPNS0_16GemmParallelInfoIiEE[__ZN5Eigen8internal29general_matrix_matrix_productIidLi0ELb0EdLi0ELb0ELi0EE3runEiiiPKdiS4_iPdidRNS0_15level3_blockingIddEEPNS0_16GemmParallelInfoIiEE]+0x41): undefined reference to omp_get_thread_num' C:/rtools40/mingw32/bin/../lib/gcc/i686-w64-mingw32/8.3.0/../../../../i686-w64-mingw32/bin/ld.exe: SciBet.o:SciBet.cpp:(.text$_ZN5Eigen8internal29general_matrix_matrix_productIidLi0ELb0EdLi0ELb0ELi0EE3runEiiiPKdiS4_iPdidRNS0_15level3_blockingIddEEPNS0_16GemmParallelInfoIiEE[__ZN5Eigen8internal29general_matrix_matrix_productIidLi0ELb0EdLi0ELb0ELi0EE3runEiiiPKdiS4_iPdidRNS0_15level3_blockingIddEEPNS0_16GemmParallelInfoIiEE]+0x49): undefined reference to omp_get_num_threads'
C:/rtools40/mingw32/bin/../lib/gcc/i686-w64-mingw32/8.3.0/../../../../i686-w64-mingw32/bin/ld.exe: SciBet.o:SciBet.cpp:(.text$_ZN5Eigen8internal16parallelize_gemmILb1ENS0_12gemm_functorIdiNS0_29general_matrix_matrix_productIidLi0ELb0EdLi0ELb0ELi0EEENS_3MapINS_6MatrixIdLin1ELin1ELi0ELin1ELin1EEELi0ENS_6StrideILi0ELi0EEEEESA_S7_NS0_19gemm_blocking_spaceILi0EddLin1ELin1ELin1ELi1ELb0EEEEEiEEvRKT0_T1_SH_SH_b[__ZN5Eigen8internal16parallelize_gemmILb1ENS0_12gemm_functorIdiNS0_29general_matrix_matrix_productIidLi0ELb0EdLi0ELb0ELi0EEENS_3MapINS_6MatrixIdLin1ELin1ELi0ELin1ELin1EEELi0ENS_6StrideILi0ELi0EEEEESA_S7_NS0_19gemm_blocking_spaceILi0EddLin1ELin1ELin1ELi1ELb0EEEEEiEEvRKT0_T1_SH_SH_b]+0x7e): undefined reference to omp_get_num_threads' C:/rtools40/mingw32/bin/../lib/gcc/i686-w64-mingw32/8.3.0/../../../../i686-w64-mingw32/bin/ld.exe: SciBet.o:SciBet.cpp:(.text$_ZN5Eigen8internal16parallelize_gemmILb1ENS0_12gemm_functorIdiNS0_29general_matrix_matrix_productIidLi0ELb0EdLi0ELb0ELi0EEENS_3MapINS_6MatrixIdLin1ELin1ELi0ELin1ELin1EEELi0ENS_6StrideILi0ELi0EEEEESA_S7_NS0_19gemm_blocking_spaceILi0EddLin1ELin1ELin1ELi1ELb0EEEEEiEEvRKT0_T1_SH_SH_b[__ZN5Eigen8internal16parallelize_gemmILb1ENS0_12gemm_functorIdiNS0_29general_matrix_matrix_productIidLi0ELb0EdLi0ELb0ELi0EEENS_3MapINS_6MatrixIdLin1ELin1ELi0ELin1ELin1EEELi0ENS_6StrideILi0ELi0EEEEESA_S7_NS0_19gemm_blocking_spaceILi0EddLin1ELin1ELin1ELi1ELb0EEEEEiEEvRKT0_T1_SH_SH_b]+0x229): undefined reference to GOMP_parallel'
C:/rtools40/mingw32/bin/../lib/gcc/i686-w64-mingw32/8.3.0/../../../../i686-w64-mingw32/bin/ld.exe: SciBet.o:SciBet.cpp:(.text$_ZN5Eigen8internal16parallelize_gemmILb1ENS0_12gemm_functorIdiNS0_29general_matrix_matrix_productIidLi0ELb0EdLi0ELb0ELi0EEENS_3MapINS_6MatrixIdLin1ELin1ELi0ELin1ELin1EEELi0ENS_6StrideILi0ELi0EEEEESA_S7_NS0_19gemm_blocking_spaceILi0EddLin1ELin1ELin1ELi1ELb0EEEEEiEEvRKT0_T1_SH_SH_b[__ZN5Eigen8internal16parallelize_gemmILb1ENS0_12gemm_functorIdiNS0_29general_matrix_matrix_productIidLi0ELb0EdLi0ELb0ELi0EEENS_3MapINS_6MatrixIdLin1ELin1ELi0ELin1ELin1EEELi0ENS_6StrideILi0ELi0EEEEESA_S7_NS0_19gemm_blocking_spaceILi0EddLin1ELin1ELin1ELi1ELb0EEEEEiEEvRKT0_T1_SH_SH_b]+0x2b6): undefined reference to omp_get_max_threads' C:/rtools40/mingw32/bin/../lib/gcc/i686-w64-mingw32/8.3.0/../../../../i686-w64-mingw32/bin/ld.exe: SciBet.o:SciBet.cpp:(.text$_ZN5Eigen8internal16parallelize_gemmILb1ENS0_12gemm_functorIdiNS0_29general_matrix_matrix_productIidLi0ELb0EdLi0ELb0ELi0EEENS_3MapINS_6MatrixIdLin1ELin1ELi0ELin1ELin1EEELi0ENS_6StrideILi0ELi0EEEEESA_S7_NS0_19gemm_blocking_spaceILi0EddLin1ELin1ELin1ELi1ELb0EEEEEiEEvRKT0_T1_SH_SH_b[__ZN5Eigen8internal16parallelize_gemmILb1ENS0_12gemm_functorIdiNS0_29general_matrix_matrix_productIidLi0ELb0EdLi0ELb0ELi0EEENS_3MapINS_6MatrixIdLin1ELin1ELi0ELin1ELin1EEELi0ENS_6StrideILi0ELi0EEEEESA_S7_NS0_19gemm_blocking_spaceILi0EddLin1ELin1ELin1ELi1ELb0EEEEEiEEvRKT0_T1_SH_SH_b]+0x309): undefined reference to GOMP_parallel'
C:/rtools40/mingw32/bin/../lib/gcc/i686-w64-mingw32/8.3.0/../../../../i686-w64-mingw32/bin/ld.exe: SciBet.o:SciBet.cpp:(.text$_ZN5Eigen8internal16parallelize_gemmILb1ENS0_12gemm_functorIdiNS0_29general_matrix_matrix_productIidLi0ELb0EdLi0ELb0ELi0EEENS_3MapINS_6MatrixIdLin1ELin1ELi0ELin1ELin1EEELi0ENS_6StrideILi0ELi0EEEEESA_S7_NS0_19gemm_blocking_spaceILi0EddLin1ELin1ELin1ELi1ELb0EEEEEiEEvRKT0_T1_SH_SH_b[__ZN5Eigen8internal16parallelize_gemmILb1ENS0_12gemm_functorIdiNS0_29general_matrix_matrix_productIidLi0ELb0EdLi0ELb0ELi0EEENS_3MapINS_6MatrixIdLin1ELin1ELi0ELin1ELin1EEELi0ENS_6StrideILi0ELi0EEEEESA_S7_NS0_19gemm_blocking_spaceILi0EddLin1ELin1ELin1ELi1ELb0EEEEEiEEvRKT0_T1_SH_SH_b]+0x471): undefined reference to omp_get_max_threads' C:/rtools40/mingw32/bin/../lib/gcc/i686-w64-mingw32/8.3.0/../../../../i686-w64-mingw32/bin/ld.exe: SciBet.o:SciBet.cpp:(.text$_ZN5Eigen8internal16parallelize_gemmILb1ENS0_12gemm_functorIdiNS0_29general_matrix_matrix_productIidLi0ELb0EdLi0ELb0ELi0EEENS_3MapINS_6MatrixIdLin1ELin1ELi0ELin1ELin1EEELi0ENS_6StrideILi0ELi0EEEEESA_S7_NS0_19gemm_blocking_spaceILi0EddLin1ELin1ELin1ELi1ELb0EEEEEiEEvRKT0_T1_SH_SH_b[__ZN5Eigen8internal16parallelize_gemmILb1ENS0_12gemm_functorIdiNS0_29general_matrix_matrix_productIidLi0ELb0EdLi0ELb0ELi0EEENS_3MapINS_6MatrixIdLin1ELin1ELi0ELin1ELin1EEELi0ENS_6StrideILi0ELi0EEEEESA_S7_NS0_19gemm_blocking_spaceILi0EddLin1ELin1ELin1ELi1ELb0EEEEEiEEvRKT0_T1_SH_SH_b]+0x4b5): undefined reference to GOMP_parallel'
collect2.exe: error: ld returned 1 exit status
no DLL was created
ERROR: compilation failed for package 'scibet'

  • removing 'C:/Program Files/R/R-4.0.0/library/scibet'

C:\Program Files\R\R-4.0.0\bin>gcc --version
gcc (tdm-1) 5.1.0
Copyright (C) 2015 Free Software Foundation, Inc.
This is free software; see the source for copying conditions. There is NO
warranty; not even for MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.

@nicheng-wjq
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Installing it on windows is not successful:
C:/rtools40/mingw32/bin/g++ -std=gnu++11 -shared -s -static-libgcc -o scibet.dll tmp.def RcppExports.o SciBet.o -LC:/PROGRA1/R/R-401.0/bin/i386 -lR
C:/rtools40/mingw32/bin/../lib/gcc/i686-w64-mingw32/8.3.0/../../../../i686-w64-mingw32/bin/ld.exe: SciBet.o:SciBet.cpp:(.text+0x18): undefined reference to omp_get_num_threads' C:/rtools40/mingw32/bin/../lib/gcc/i686-w64-mingw32/8.3.0/../../../../i686-w64-mingw32/bin/ld.exe: SciBet.o:SciBet.cpp:(.text+0x23): undefined reference to omp_get_thread_num'
C:/rtools40/mingw32/bin/../lib/gcc/i686-w64-mingw32/8.3.0/../../../../i686-w64-mingw32/bin/ld.exe: SciBet.o:SciBet.cpp:(.text+0x258): undefined reference to omp_get_num_threads' C:/rtools40/mingw32/bin/../lib/gcc/i686-w64-mingw32/8.3.0/../../../../i686-w64-mingw32/bin/ld.exe: SciBet.o:SciBet.cpp:(.text+0x263): undefined reference to omp_get_thread_num'
C:/rtools40/mingw32/bin/../lib/gcc/i686-w64-mingw32/8.3.0/../../../../i686-w64-mingw32/bin/ld.exe: SciBet.o:SciBet.cpp:(.text+0x356): undefined reference to omp_get_num_threads' C:/rtools40/mingw32/bin/../lib/gcc/i686-w64-mingw32/8.3.0/../../../../i686-w64-mingw32/bin/ld.exe: SciBet.o:SciBet.cpp:(.text+0x35d): undefined reference to omp_get_thread_num'
C:/rtools40/mingw32/bin/../lib/gcc/i686-w64-mingw32/8.3.0/../../../../i686-w64-mingw32/bin/ld.exe: SciBet.o:SciBet.cpp:(.text+0x478): undefined reference to omp_get_num_threads' C:/rtools40/mingw32/bin/../lib/gcc/i686-w64-mingw32/8.3.0/../../../../i686-w64-mingw32/bin/ld.exe: SciBet.o:SciBet.cpp:(.text+0x483): undefined reference to omp_get_thread_num'
C:/rtools40/mingw32/bin/../lib/gcc/i686-w64-mingw32/8.3.0/../../../../i686-w64-mingw32/bin/ld.exe: SciBet.o:SciBet.cpp:(.text+0x5e8): undefined reference to omp_get_num_threads' C:/rtools40/mingw32/bin/../lib/gcc/i686-w64-mingw32/8.3.0/../../../../i686-w64-mingw32/bin/ld.exe: SciBet.o:SciBet.cpp:(.text+0x5f3): undefined reference to omp_get_thread_num'
C:/rtools40/mingw32/bin/../lib/gcc/i686-w64-mingw32/8.3.0/../../../../i686-w64-mingw32/bin/ld.exe: SciBet.o:SciBet.cpp:(.text+0x808): undefined reference to omp_get_num_threads' C:/rtools40/mingw32/bin/../lib/gcc/i686-w64-mingw32/8.3.0/../../../../i686-w64-mingw32/bin/ld.exe: SciBet.o:SciBet.cpp:(.text+0x813): undefined reference to omp_get_thread_num'
C:/rtools40/mingw32/bin/../lib/gcc/i686-w64-mingw32/8.3.0/../../../../i686-w64-mingw32/bin/ld.exe: SciBet.o:SciBet.cpp:(.text+0x9ad): undefined reference to omp_get_num_threads' C:/rtools40/mingw32/bin/../lib/gcc/i686-w64-mingw32/8.3.0/../../../../i686-w64-mingw32/bin/ld.exe: SciBet.o:SciBet.cpp:(.text+0x9b4): undefined reference to omp_get_thread_num'
C:/rtools40/mingw32/bin/../lib/gcc/i686-w64-mingw32/8.3.0/../../../../i686-w64-mingw32/bin/ld.exe: SciBet.o:SciBet.cpp:(.text+0xf30): undefined reference to GOMP_parallel' C:/rtools40/mingw32/bin/../lib/gcc/i686-w64-mingw32/8.3.0/../../../../i686-w64-mingw32/bin/ld.exe: SciBet.o:SciBet.cpp:(.text+0x101f): undefined reference to GOMP_parallel'
C:/rtools40/mingw32/bin/../lib/gcc/i686-w64-mingw32/8.3.0/../../../../i686-w64-mingw32/bin/ld.exe: SciBet.o:SciBet.cpp:(.text+0x13b5): undefined reference to omp_set_num_threads' C:/rtools40/mingw32/bin/../lib/gcc/i686-w64-mingw32/8.3.0/../../../../i686-w64-mingw32/bin/ld.exe: SciBet.o:SciBet.cpp:(.text+0x1808): undefined reference to omp_get_num_threads'
C:/rtools40/mingw32/bin/../lib/gcc/i686-w64-mingw32/8.3.0/../../../../i686-w64-mingw32/bin/ld.exe: SciBet.o:SciBet.cpp:(.text+0x180f): undefined reference to omp_get_thread_num' C:/rtools40/mingw32/bin/../lib/gcc/i686-w64-mingw32/8.3.0/../../../../i686-w64-mingw32/bin/ld.exe: SciBet.o:SciBet.cpp:(.text+0x1d6c): undefined reference to GOMP_parallel'
C:/rtools40/mingw32/bin/../lib/gcc/i686-w64-mingw32/8.3.0/../../../../i686-w64-mingw32/bin/ld.exe: SciBet.o:SciBet.cpp:(.text+0x23fd): undefined reference to omp_set_num_threads' C:/rtools40/mingw32/bin/../lib/gcc/i686-w64-mingw32/8.3.0/../../../../i686-w64-mingw32/bin/ld.exe: SciBet.o:SciBet.cpp:(.text+0x267f): undefined reference to GOMP_parallel'
C:/rtools40/mingw32/bin/../lib/gcc/i686-w64-mingw32/8.3.0/../../../../i686-w64-mingw32/bin/ld.exe: SciBet.o:SciBet.cpp:(.text+0x29fe): undefined reference to omp_get_thread_num' C:/rtools40/mingw32/bin/../lib/gcc/i686-w64-mingw32/8.3.0/../../../../i686-w64-mingw32/bin/ld.exe: SciBet.o:SciBet.cpp:(.text+0x2a05): undefined reference to omp_get_num_threads'
C:/rtools40/mingw32/bin/../lib/gcc/i686-w64-mingw32/8.3.0/../../../../i686-w64-mingw32/bin/ld.exe: SciBet.o:SciBet.cpp:(.text+0x2e64): undefined reference to GOMP_parallel' C:/rtools40/mingw32/bin/../lib/gcc/i686-w64-mingw32/8.3.0/../../../../i686-w64-mingw32/bin/ld.exe: SciBet.o:SciBet.cpp:(.text+0x2f49): undefined reference to omp_set_num_threads'
C:/rtools40/mingw32/bin/../lib/gcc/i686-w64-mingw32/8.3.0/../../../../i686-w64-mingw32/bin/ld.exe: SciBet.o:SciBet.cpp:(.text+0x3a00): undefined reference to GOMP_parallel' C:/rtools40/mingw32/bin/../lib/gcc/i686-w64-mingw32/8.3.0/../../../../i686-w64-mingw32/bin/ld.exe: SciBet.o:SciBet.cpp:(.text+0x3aa7): undefined reference to omp_set_num_threads'
C:/rtools40/mingw32/bin/../lib/gcc/i686-w64-mingw32/8.3.0/../../../../i686-w64-mingw32/bin/ld.exe: SciBet.o:SciBet.cpp:(.text+0x40f3): undefined reference to GOMP_parallel' C:/rtools40/mingw32/bin/../lib/gcc/i686-w64-mingw32/8.3.0/../../../../i686-w64-mingw32/bin/ld.exe: SciBet.o:SciBet.cpp:(.text+0x42be): undefined reference to GOMP_parallel'
C:/rtools40/mingw32/bin/../lib/gcc/i686-w64-mingw32/8.3.0/../../../../i686-w64-mingw32/bin/ld.exe: SciBet.o:SciBet.cpp:(.text+0x4504): undefined reference to omp_set_num_threads' C:/rtools40/mingw32/bin/../lib/gcc/i686-w64-mingw32/8.3.0/../../../../i686-w64-mingw32/bin/ld.exe: SciBet.o:SciBet.cpp:(.text+0x45e0): undefined reference to GOMP_parallel'
C:/rtools40/mingw32/bin/../lib/gcc/i686-w64-mingw32/8.3.0/../../../../i686-w64-mingw32/bin/ld.exe: SciBet.o:SciBet.cpp:(.text$_ZN5Eigen8internal29general_matrix_matrix_productIidLi0ELb0EdLi0ELb0ELi0EE3runEiiiPKdiS4_iPdidRNS0_15level3_blockingIddEEPNS0_16GemmParallelInfoIiEE[__ZN5Eigen8internal29general_matrix_matrix_productIidLi0ELb0EdLi0ELb0ELi0EE3runEiiiPKdiS4_iPdidRNS0_15level3_blockingIddEEPNS0_16GemmParallelInfoIiEE]+0x41): undefined reference to omp_get_thread_num' C:/rtools40/mingw32/bin/../lib/gcc/i686-w64-mingw32/8.3.0/../../../../i686-w64-mingw32/bin/ld.exe: SciBet.o:SciBet.cpp:(.text$_ZN5Eigen8internal29general_matrix_matrix_productIidLi0ELb0EdLi0ELb0ELi0EE3runEiiiPKdiS4_iPdidRNS0_15level3_blockingIddEEPNS0_16GemmParallelInfoIiEE[__ZN5Eigen8internal29general_matrix_matrix_productIidLi0ELb0EdLi0ELb0ELi0EE3runEiiiPKdiS4_iPdidRNS0_15level3_blockingIddEEPNS0_16GemmParallelInfoIiEE]+0x49): undefined reference to omp_get_num_threads'
C:/rtools40/mingw32/bin/../lib/gcc/i686-w64-mingw32/8.3.0/../../../../i686-w64-mingw32/bin/ld.exe: SciBet.o:SciBet.cpp:(.text$_ZN5Eigen8internal16parallelize_gemmILb1ENS0_12gemm_functorIdiNS0_29general_matrix_matrix_productIidLi0ELb0EdLi0ELb0ELi0EEENS_3MapINS_6MatrixIdLin1ELin1ELi0ELin1ELin1EEELi0ENS_6StrideILi0ELi0EEEEESA_S7_NS0_19gemm_blocking_spaceILi0EddLin1ELin1ELin1ELi1ELb0EEEEEiEEvRKT0_T1_SH_SH_b[__ZN5Eigen8internal16parallelize_gemmILb1ENS0_12gemm_functorIdiNS0_29general_matrix_matrix_productIidLi0ELb0EdLi0ELb0ELi0EEENS_3MapINS_6MatrixIdLin1ELin1ELi0ELin1ELin1EEELi0ENS_6StrideILi0ELi0EEEEESA_S7_NS0_19gemm_blocking_spaceILi0EddLin1ELin1ELin1ELi1ELb0EEEEEiEEvRKT0_T1_SH_SH_b]+0x7e): undefined reference to omp_get_num_threads' C:/rtools40/mingw32/bin/../lib/gcc/i686-w64-mingw32/8.3.0/../../../../i686-w64-mingw32/bin/ld.exe: SciBet.o:SciBet.cpp:(.text$_ZN5Eigen8internal16parallelize_gemmILb1ENS0_12gemm_functorIdiNS0_29general_matrix_matrix_productIidLi0ELb0EdLi0ELb0ELi0EEENS_3MapINS_6MatrixIdLin1ELin1ELi0ELin1ELin1EEELi0ENS_6StrideILi0ELi0EEEEESA_S7_NS0_19gemm_blocking_spaceILi0EddLin1ELin1ELin1ELi1ELb0EEEEEiEEvRKT0_T1_SH_SH_b[__ZN5Eigen8internal16parallelize_gemmILb1ENS0_12gemm_functorIdiNS0_29general_matrix_matrix_productIidLi0ELb0EdLi0ELb0ELi0EEENS_3MapINS_6MatrixIdLin1ELin1ELi0ELin1ELin1EEELi0ENS_6StrideILi0ELi0EEEEESA_S7_NS0_19gemm_blocking_spaceILi0EddLin1ELin1ELin1ELi1ELb0EEEEEiEEvRKT0_T1_SH_SH_b]+0x229): undefined reference to GOMP_parallel'
C:/rtools40/mingw32/bin/../lib/gcc/i686-w64-mingw32/8.3.0/../../../../i686-w64-mingw32/bin/ld.exe: SciBet.o:SciBet.cpp:(.text$_ZN5Eigen8internal16parallelize_gemmILb1ENS0_12gemm_functorIdiNS0_29general_matrix_matrix_productIidLi0ELb0EdLi0ELb0ELi0EEENS_3MapINS_6MatrixIdLin1ELin1ELi0ELin1ELin1EEELi0ENS_6StrideILi0ELi0EEEEESA_S7_NS0_19gemm_blocking_spaceILi0EddLin1ELin1ELin1ELi1ELb0EEEEEiEEvRKT0_T1_SH_SH_b[__ZN5Eigen8internal16parallelize_gemmILb1ENS0_12gemm_functorIdiNS0_29general_matrix_matrix_productIidLi0ELb0EdLi0ELb0ELi0EEENS_3MapINS_6MatrixIdLin1ELin1ELi0ELin1ELin1EEELi0ENS_6StrideILi0ELi0EEEEESA_S7_NS0_19gemm_blocking_spaceILi0EddLin1ELin1ELin1ELi1ELb0EEEEEiEEvRKT0_T1_SH_SH_b]+0x2b6): undefined reference to omp_get_max_threads' C:/rtools40/mingw32/bin/../lib/gcc/i686-w64-mingw32/8.3.0/../../../../i686-w64-mingw32/bin/ld.exe: SciBet.o:SciBet.cpp:(.text$_ZN5Eigen8internal16parallelize_gemmILb1ENS0_12gemm_functorIdiNS0_29general_matrix_matrix_productIidLi0ELb0EdLi0ELb0ELi0EEENS_3MapINS_6MatrixIdLin1ELin1ELi0ELin1ELin1EEELi0ENS_6StrideILi0ELi0EEEEESA_S7_NS0_19gemm_blocking_spaceILi0EddLin1ELin1ELin1ELi1ELb0EEEEEiEEvRKT0_T1_SH_SH_b[__ZN5Eigen8internal16parallelize_gemmILb1ENS0_12gemm_functorIdiNS0_29general_matrix_matrix_productIidLi0ELb0EdLi0ELb0ELi0EEENS_3MapINS_6MatrixIdLin1ELin1ELi0ELin1ELin1EEELi0ENS_6StrideILi0ELi0EEEEESA_S7_NS0_19gemm_blocking_spaceILi0EddLin1ELin1ELin1ELi1ELb0EEEEEiEEvRKT0_T1_SH_SH_b]+0x309): undefined reference to GOMP_parallel'
C:/rtools40/mingw32/bin/../lib/gcc/i686-w64-mingw32/8.3.0/../../../../i686-w64-mingw32/bin/ld.exe: SciBet.o:SciBet.cpp:(.text$_ZN5Eigen8internal16parallelize_gemmILb1ENS0_12gemm_functorIdiNS0_29general_matrix_matrix_productIidLi0ELb0EdLi0ELb0ELi0EEENS_3MapINS_6MatrixIdLin1ELin1ELi0ELin1ELin1EEELi0ENS_6StrideILi0ELi0EEEEESA_S7_NS0_19gemm_blocking_spaceILi0EddLin1ELin1ELin1ELi1ELb0EEEEEiEEvRKT0_T1_SH_SH_b[__ZN5Eigen8internal16parallelize_gemmILb1ENS0_12gemm_functorIdiNS0_29general_matrix_matrix_productIidLi0ELb0EdLi0ELb0ELi0EEENS_3MapINS_6MatrixIdLin1ELin1ELi0ELin1ELin1EEELi0ENS_6StrideILi0ELi0EEEEESA_S7_NS0_19gemm_blocking_spaceILi0EddLin1ELin1ELin1ELi1ELb0EEEEEiEEvRKT0_T1_SH_SH_b]+0x471): undefined reference to omp_get_max_threads' C:/rtools40/mingw32/bin/../lib/gcc/i686-w64-mingw32/8.3.0/../../../../i686-w64-mingw32/bin/ld.exe: SciBet.o:SciBet.cpp:(.text$_ZN5Eigen8internal16parallelize_gemmILb1ENS0_12gemm_functorIdiNS0_29general_matrix_matrix_productIidLi0ELb0EdLi0ELb0ELi0EEENS_3MapINS_6MatrixIdLin1ELin1ELi0ELin1ELin1EEELi0ENS_6StrideILi0ELi0EEEEESA_S7_NS0_19gemm_blocking_spaceILi0EddLin1ELin1ELin1ELi1ELb0EEEEEiEEvRKT0_T1_SH_SH_b[__ZN5Eigen8internal16parallelize_gemmILb1ENS0_12gemm_functorIdiNS0_29general_matrix_matrix_productIidLi0ELb0EdLi0ELb0ELi0EEENS_3MapINS_6MatrixIdLin1ELin1ELi0ELin1ELin1EEELi0ENS_6StrideILi0ELi0EEEEESA_S7_NS0_19gemm_blocking_spaceILi0EddLin1ELin1ELin1ELi1ELb0EEEEEiEEvRKT0_T1_SH_SH_b]+0x4b5): undefined reference to GOMP_parallel'
collect2.exe: error: ld returned 1 exit status
no DLL was created
ERROR: compilation failed for package 'scibet'

  • removing 'C:/Program Files/R/R-4.0.0/library/scibet'

C:\Program Files\R\R-4.0.0\bin>gcc --version
gcc (tdm-1) 5.1.0
Copyright (C) 2015 Free Software Foundation, Inc.
This is free software; see the source for copying conditions. There is NO
warranty; not even for MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.

I had the same problem!!

@PaulingLiu
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openmp, which is required for parallel applications, should be installed in your windows. Please refer to https://blog.csdn.net/dreamer_blue/article/details/51755767.

@r-melo
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r-melo commented May 19, 2020

I have the same issue, installed tdm_gcc and the issue persists. I also installed intel_openmp via anaconda, and couldn't solve it.

@hxretlcw
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We are now developing a pure R implementation of SciBet, which will be useful for Windows users and will be released in 2~3 weeks.

@Landau1994
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Wonderful! I am looking forward to the updates

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@Landau1994 @hxretlcw @zhoux85 @nicheng-wjq @r-melo @PaulingLiu