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PaulingLiu / scibet

A portable and fast single cell type identifier
BSD 3-Clause "New" or "Revised" License
62 stars 11 forks source link

Installation Failed #12

Closed tomyputw closed 3 months ago

tomyputw commented 3 months ago

I install it from github and found that it install from source. I work in windows and I read the close issue. I try to add GCC to environment path but does not work, return errors and sessionInfo as follows. I am sorry for I dont know how to use markdown to present it.

C:\Program Files\rtools43\x86_64-w64-mingw32.static.posix\bin/ld.exe: SciBet.o:SciBet.cpp:(.text$_ZN5Eigen8internal16parallelize_gemmILb1ENS0_12gemm_functorIdxNS0_29general_matrix_matrix_productIxdLi0ELb0EdLi0ELb0ELi0ELi1EEENS_3MapINS_6MatrixIdLin1ELin1ELi0ELin1ELin1EEELi0ENS_6StrideILi0ELi0EEEEESA_S7_NS0_19gemm_blocking_spaceILi0EddLin1ELin1ELin1ELi1ELb0EEEEExEEvRKT0_T1_SH_SH_b[_ZN5Eigen8internal16parallelize_gemmILb1ENS0_12gemm_functorIdxNS0_29general_matrix_matrix_productIxdLi0ELb0EdLi0ELb0ELi0ELi1EEENS_3MapINS_6MatrixIdLin1ELin1ELi0ELin1ELin1EEELi0ENS_6StrideILi0ELi0EEEEESA_S7_NS0_19gemm_blocking_spaceILi0EddLin1ELin1ELin1ELi1ELb0EEEEExEEvRKT0_T1_SH_SH_b]+0x124): undefined reference to omp_get_max_threads' C:\Program Files\rtools43\x86_64-w64-mingw32.static.posix\bin/ld.exe: SciBet.o:SciBet.cpp:(.text$_ZN5Eigen8internal16parallelize_gemmILb1ENS0_12gemm_functorIdxNS0_29general_matrix_matrix_productIxdLi0ELb0EdLi0ELb0ELi0ELi1EEENS_3MapINS_6MatrixIdLin1ELin1ELi0ELin1ELin1EEELi0ENS_6StrideILi0ELi0EEEEESA_S7_NS0_19gemm_blocking_spaceILi0EddLin1ELin1ELin1ELi1ELb0EEEEExEEvRKT0_T1_SH_SH_b[_ZN5Eigen8internal16parallelize_gemmILb1ENS0_12gemm_functorIdxNS0_29general_matrix_matrix_productIxdLi0ELb0EdLi0ELb0ELi0ELi1EEENS_3MapINS_6MatrixIdLin1ELin1ELi0ELin1ELin1EEELi0ENS_6StrideILi0ELi0EEEEESA_S7_NS0_19gemm_blocking_spaceILi0EddLin1ELin1ELin1ELi1ELb0EEEEExEEvRKT0_T1_SH_SH_b]+0x139): undefined reference toomp_get_num_threads' C:\Program Files\rtools43\x86_64-w64-mingw32.static.posix\bin/ld.exe: SciBet.o:SciBet.cpp:(.text$_ZN5Eigen8internal16parallelize_gemmILb1ENS0_12gemm_functorIdxNS0_29general_matrix_matrix_productIxdLi0ELb0EdLi0ELb0ELi0ELi1EEENS_3MapINS_6MatrixIdLin1ELin1ELi0ELin1ELin1EEELi0ENS_6StrideILi0ELi0EEEEESA_S7_NS0_19gemm_blocking_spaceILi0EddLin1ELin1ELin1ELi1ELb0EEEEExEEvRKT0_T1_SH_SH_b[_ZN5Eigen8internal16parallelize_gemmILb1ENS0_12gemm_functorIdxNS0_29general_matrix_matrix_productIxdLi0ELb0EdLi0ELb0ELi0ELi1EEENS_3MapINS_6MatrixIdLin1ELin1ELi0ELin1ELin1EEELi0ENS_6StrideILi0ELi0EEEEESA_S7_NS0_19gemm_blocking_spaceILi0EddLin1ELin1ELin1ELi1ELb0EEEEExEEvRKT0_T1_SH_SH_b]+0x264): undefined reference to GOMP_parallel' C:\Program Files\rtools43\x86_64-w64-mingw32.static.posix\bin/ld.exe: SciBet.o:SciBet.cpp:(.text$_ZN5Eigen8internal16parallelize_gemmILb1ENS0_12gemm_functorIdxNS0_29general_matrix_matrix_productIxdLi0ELb0EdLi0ELb0ELi0ELi1EEENS_3MapINS_6MatrixIdLin1ELin1ELi0ELin1ELin1EEELi0ENS_6StrideILi0ELi0EEEEESA_S7_NS0_19gemm_blocking_spaceILi0EddLin1ELin1ELin1ELi1ELb0EEEEExEEvRKT0_T1_SH_SH_b[_ZN5Eigen8internal16parallelize_gemmILb1ENS0_12gemm_functorIdxNS0_29general_matrix_matrix_productIxdLi0ELb0EdLi0ELb0ELi0ELi1EEENS_3MapINS_6MatrixIdLin1ELin1ELi0ELin1ELin1EEELi0ENS_6StrideILi0ELi0EEEEESA_S7_NS0_19gemm_blocking_spaceILi0EddLin1ELin1ELin1ELi1ELb0EEEEExEEvRKT0_T1_SH_SH_b]+0x2f1): undefined reference toGOMP_parallel' C:\Program Files\rtools43\x86_64-w64-mingw32.static.posix\bin/ld.exe: SciBet.o:SciBet.cpp:(.text$_ZN5Eigen8internal16parallelize_gemmILb1ENS0_12gemm_functorIdxNS0_29general_matrix_matrix_productIxdLi0ELb0EdLi0ELb0ELi0ELi1EEENS_3MapINS_6MatrixIdLin1ELin1ELi0ELin1ELin1EEELi0ENS_6StrideILi0ELi0EEEEESA_S7_NS0_19gemm_blocking_spaceILi0EddLin1ELin1ELin1ELi1ELb0EEEEExEEvRKT0_T1_SH_SH_b[_ZN5Eigen8internal16parallelize_gemmILb1ENS0_12gemm_functorIdxNS0_29general_matrix_matrix_productIxdLi0ELb0EdLi0ELb0ELi0ELi1EEENS_3MapINS_6MatrixIdLin1ELin1ELi0ELin1ELin1EEELi0ENS_6StrideILi0ELi0EEEEESA_S7_NS0_19gemm_blocking_spaceILi0EddLin1ELin1ELin1ELi1ELb0EEEEExEEvRKT0_T1_SH_SH_b]+0x385): undefined reference to GOMP_parallel' C:\Program Files\rtools43\x86_64-w64-mingw32.static.posix\bin/ld.exe: SciBet.o:SciBet.cpp:(.text$_ZN5Eigen8internal16parallelize_gemmILb1ENS0_12gemm_functorIdxNS0_29general_matrix_matrix_productIxdLi0ELb0EdLi0ELb0ELi0ELi1EEENS_3MapINS_6MatrixIdLin1ELin1ELi0ELin1ELin1EEELi0ENS_6StrideILi0ELi0EEEEESA_S7_NS0_19gemm_blocking_spaceILi0EddLin1ELin1ELin1ELi1ELb0EEEEExEEvRKT0_T1_SH_SH_b[_ZN5Eigen8internal16parallelize_gemmILb1ENS0_12gemm_functorIdxNS0_29general_matrix_matrix_productIxdLi0ELb0EdLi0ELb0ELi0ELi1EEENS_3MapINS_6MatrixIdLin1ELin1ELi0ELin1ELin1EEELi0ENS_6StrideILi0ELi0EEEEESA_S7_NS0_19gemm_blocking_spaceILi0EddLin1ELin1ELin1ELi1ELb0EEEEExEEvRKT0_T1_SH_SH_b]+0x429): undefined reference toomp_get_max_threads' C:\Program Files\rtools43\x86_64-w64-mingw32.static.posix\bin/ld.exe: SciBet.o:SciBet.cpp:(.text$_ZN5Eigen8internal16parallelize_gemmILb1ENS0_12gemm_functorIdxNS0_29general_matrix_matrix_productIxdLi0ELb0EdLi0ELb0ELi0ELi1EEENS_3MapINS_6MatrixIdLin1ELin1ELi0ELin1ELin1EEELi0ENS_6StrideILi0ELi0EEEEESA_S7_NS0_19gemm_blocking_spaceILi0EddLin1ELin1ELin1ELi1ELb0EEEEExEEvRKT0_T1_SH_SH_b[_ZN5Eigen8internal16parallelize_gemmILb1ENS0_12gemm_functorIdxNS0_29general_matrix_matrix_productIxdLi0ELb0EdLi0ELb0ELi0ELi1EEENS_3MapINS_6MatrixIdLin1ELin1ELi0ELin1ELin1EEELi0ENS_6StrideILi0ELi0EEEEESA_S7_NS0_19gemm_blocking_spaceILi0EddLin1ELin1ELin1ELi1ELb0EEEEExEEvRKT0_T1_SH_SH_b]+0x49d): undefined reference to `GOMP_parallel' collect2.exe: error: ld returned 1 exit status no DLL was created ERROR: compilation failed for package 'scibet'

tomyputw commented 3 months ago

sessionInfo() R version 4.3.0 (2023-04-21 ucrt) Platform: x86_64-w64-mingw32/x64 (64-bit) Running under: Windows 10 x64 (build 17763)

Matrix products: default

locale: [1] LC_COLLATE=Chinese (Simplified)_China.936 LC_CTYPE=Chinese (Simplified)_China.936
[3] LC_MONETARY=Chinese (Simplified)_China.936 LC_NUMERIC=C
[5] LC_TIME=Chinese (Simplified)_China.936

time zone: Asia/Shanghai tzcode source: internal

attached base packages: [1] stats graphics grDevices utils datasets methods base

other attached packages: [1] scibetR_0.1.0 Seurat_5.0.3 SeuratObject_5.0.1 sp_2.1-3 scClassify_1.5.1

loaded via a namespace (and not attached): [1] segmented_2.0-3 fs_1.6.3 matrixStats_1.2.0
[4] spatstat.sparse_3.0-3 bitops_1.0-7 devtools_2.4.5
[7] httr_1.4.7 hopach_2.64.0 RColorBrewer_1.1-3
[10] profvis_0.3.8 tools_4.3.0 sctransform_0.4.1
[13] alabaster.base_1.4.1 utf8_1.2.4 R6_2.5.1
[16] HDF5Array_1.32.0 lazyeval_0.2.2 uwot_0.1.16
[19] mgcv_1.9-1 rhdf5filters_1.16.0 urlchecker_1.0.1
[22] withr_3.0.0 gridExtra_2.3 progressr_0.14.0
[25] cli_3.6.2 Biobase_2.62.0 spatstat.explore_3.2-7
[28] fastDummies_1.7.3 alabaster.se_1.4.1 diptest_0.77-0
[31] spatstat.data_3.1-2 proxy_0.4-27 ggridges_0.5.6
[34] pbapply_1.7-2 sessioninfo_1.2.2 parallelly_1.37.1
[37] limma_3.50.3 rstudioapi_0.16.0 RSQLite_2.3.5
[40] generics_0.1.3 ica_1.0-3 spatstat.random_3.2-3
[43] dplyr_1.1.4 Matrix_1.6-5 fansi_1.0.6
[46] S4Vectors_0.42.0 abind_1.4-5 lifecycle_1.0.4
[49] yaml_2.3.8 SummarizedExperiment_1.24.0 rhdf5_2.48.0
[52] SparseArray_1.2.4 BiocFileCache_2.10.1 Rtsne_0.17
[55] grid_4.3.0 blob_1.2.4 promises_1.2.1
[58] ExperimentHub_2.10.0 crayon_1.5.3 miniUI_0.1.1.1
[61] lattice_0.22-6 cowplot_1.1.3 KEGGREST_1.34.0
[64] pillar_1.9.0 GenomicRanges_1.54.1 future.apply_1.11.2
[67] codetools_0.2-19 leiden_0.4.3.1 glue_1.7.0
[70] data.table_1.15.2 remotes_2.5.0 vctrs_0.6.5
[73] png_0.1-8 gypsum_1.0.1 spam_2.10-0
[76] gtable_0.3.5 kernlab_0.9-32 cachem_1.0.8
[79] S4Arrays_1.4.1 mime_0.12 tidygraph_1.3.1
[82] survival_3.5-8 SingleCellExperiment_1.16.0 statmod_1.5.0
[85] interactiveDisplayBase_1.32.0 ellipsis_0.3.2 fitdistrplus_1.1-11
[88] ROCR_1.0-11 nlme_3.1-164 usethis_2.2.3
[91] bit64_4.0.5 alabaster.ranges_1.4.1 filelock_1.0.3
[94] RcppAnnoy_0.0.22 GenomeInfoDb_1.38.8 irlba_2.3.5.1
[97] KernSmooth_2.23-22 colorspace_2.1-0 BiocGenerics_0.48.1
[100] DBI_1.2.2 celldex_1.14.0 processx_3.8.4
[103] tidyselect_1.2.1 proxyC_0.3.4 bit_4.0.5
[106] compiler_4.3.0 curl_5.2.1 httr2_1.0.0
[109] desc_1.4.3 DelayedArray_0.30.1 plotly_4.10.4
[112] scales_1.3.0 lmtest_0.9-40 callr_3.7.6
[115] rappdirs_0.3.3 stringr_1.5.1 digest_0.6.35
[118] goftest_1.2-3 spatstat.utils_3.0-5 mixtools_2.0.0
[121] alabaster.matrix_1.4.0 XVector_0.34.0 htmltools_0.5.8
[124] pkgconfig_2.0.3 Cepo_1.10.2 sparseMatrixStats_1.16.0
[127] MatrixGenerics_1.16.0 dbplyr_2.5.0 fastmap_1.1.1
[130] rlang_1.1.3 htmlwidgets_1.6.4 shiny_1.8.1.1
[133] DelayedMatrixStats_1.24.0 farver_2.1.2 zoo_1.8-12
[136] jsonlite_1.8.8 BiocParallel_1.36.0 RCurl_1.98-1.14
[139] magrittr_2.0.3 GenomeInfoDbData_1.2.7 dotCall64_1.1-1
[142] patchwork_1.2.0 Rhdf5lib_1.16.0 munsell_0.5.1
[145] Rcpp_1.0.12 viridis_0.6.5 reticulate_1.35.0
[148] stringi_1.8.3 alabaster.schemas_1.4.0 pROC_1.18.5
[151] ggraph_2.2.1 zlibbioc_1.40.0 MASS_7.3-60.0.1
[154] AnnotationHub_3.10.0 plyr_1.8.9 pkgbuild_1.4.4
[157] parallel_4.3.0 listenv_0.9.1 ggrepel_0.9.5
[160] deldir_2.0-4 Biostrings_2.70.3 graphlayouts_1.1.1
[163] splines_4.3.0 tensor_1.5 ps_1.7.6
[166] igraph_2.0.3 spatstat.geom_3.2-9 RcppHNSW_0.6.0
[169] pkgload_1.3.4 reshape2_1.4.4 stats4_4.3.0
[172] BiocVersion_3.18.1 RcppParallel_5.1.7 BiocManager_1.30.23
[175] tweenr_2.0.3 httpuv_1.6.14 RANN_2.6.1
[178] tidyr_1.3.1 purrr_1.0.2 polyclip_1.10-6
[181] future_1.33.2 scattermore_1.2 ggplot2_3.5.1
[184] ggforce_0.4.2 xtable_1.8-4 RSpectra_0.16-1
[187] later_1.3.2 viridisLite_0.4.2 minpack.lm_1.2-4
[190] tibble_3.2.1 memoise_2.0.1 AnnotationDbi_1.64.1
[193] IRanges_2.38.0 cluster_2.1.6 globals_0.16.3

tomyputw commented 3 months ago

I try devtools::install_github("zwj-tina/scibetR") as a alternative way and finally solve this problem (I do not analyze the difference between these code).