Liux0228
commented
7 months ago Set n=2 and nfold=2, the commond is ok, while setting nfold =5 it went wrong.
result2 <- reliability.test(X, Y, network, alpha = 0.05, family = "binomial", cell_nuType 'citation("pROC")' for a citation.
Attaching package: ‘pROC’
The following objects are masked from ‘package:stats’:
cov, smooth, var
[1] "|**************************************************|"
[1] "Perform cross-validation on X with true label"
Finished!
[1] "|**************************************************|"
[1] "Perform cross-validation on X with permutated label"
Finished!
[1] "Test statistic = 1.000"
[1] "Reliability significance test p = 0.000"
> result2 <- reliability.test(X, Y, network, alpha = 0.05, family = "binomial", cell_nu[1] "|**************************************************|"
[1] "Perform cross-validation on X with true label"
*** caught segfault ***
address (nil), cause 'memory not mapped'
Traceback:
1: NetLogC(x1i, y, alpha, lambda, nlambda, ilambda, wbeta1i, wbetaii, W$Omega, W$loc, W$nadj, p1i, N0, thresh, maxit, threshP)
2: LogL0(x, y, Omega, alpha, lambda, nlambda, rlambda, nfolds, foldid, inzero, wbeta, sgn, isd, keep.beta, thresh, maxit, threshP = 1e-05)
3: APML1(X_train, Y_train, family = "binomial", penalty = "Net", alpha = alpha, Omega = network, nlambda = 100)
4: test_logit(X, Y, network, alpha, cell_num, n, nfold)
5: reliability.test(X, Y, network, alpha = 0.05, family = "binomial", cell_num = numbers, n = 2, nfold = 5)
Possible actions:
1: abort (with core dump, if enabled)
2: normal R exit
3: exit R without saving workspace
4: exit R saving workspace
Selection: 1
R is aborting now ...
Segmentation fault (core dumped)
sessionInfo()
R version 4.2.0 (2022-04-22)
Platform: x86_64-pc-linux-gnu (64-bit)
Running under: CentOS Linux 7 (Core)
Matrix products: default
BLAS/LAPACK: /usr/local/lib64/libopenblas.so.0.3
locale:
[1] LC_CTYPE=en_US.UTF-8 LC_NUMERIC=C LC_TIME=en_US.UTF-8 LC_COLLATE=en_US.UTF-8 LC_MONETARY=en_US.UTF-8
[6] LC_MESSAGES=en_US.UTF-8 LC_PAPER=en_US.UTF-8 LC_NAME=C LC_ADDRESS=C LC_TELEPHONE=C
[11] LC_MEASUREMENT=en_US.UTF-8 LC_IDENTIFICATION=C
attached base packages:
[1] stats graphics grDevices utils datasets methods base
other attached packages:
[1] ggplot2_3.4.3 preprocessCore_1.61.0 Scissor_2.0.0 Matrix_1.6-1.1 SeuratObject_4.1.4 Seurat_4.4.0 colorout_1.2-2
loaded via a namespace (and not attached):
[1] nlme_3.1-163 matrixStats_1.0.0 spatstat.sparse_3.0-2 RcppAnnoy_0.0.21 RColorBrewer_1.1-3 httr_1.4.7
[7] sctransform_0.4.0 tools_4.2.0 utf8_1.2.3 R6_2.5.1 irlba_2.3.5.1 KernSmooth_2.23-22
[13] uwot_0.1.16 lazyeval_0.2.2 colorspace_2.1-0 withr_2.5.1 sp_2.1-0 tidyselect_1.2.0
[19] gridExtra_2.3 compiler_4.2.0 progressr_0.14.0 cli_3.6.1 spatstat.explore_3.2-3 plotly_4.10.2
[25] scales_1.2.1 lmtest_0.9-40 spatstat.data_3.0-1 ggridges_0.5.4 pbapply_1.7-2 goftest_1.2-3
[31] stringr_1.5.0 digest_0.6.33 spatstat.utils_3.0-3 pkgconfig_2.0.3 htmltools_0.5.6 parallelly_1.36.0
[37] fastmap_1.1.1 htmlwidgets_1.6.2 rlang_1.1.1 shiny_1.7.5 generics_0.1.3 zoo_1.8-12
[43] jsonlite_1.8.7 spatstat.random_3.1-6 ica_1.0-3 dplyr_1.1.3 magrittr_2.0.3 patchwork_1.1.3
[49] Rcpp_1.0.11 munsell_0.5.0 fansi_1.0.4 abind_1.4-5 reticulate_1.32.0 lifecycle_1.0.3
[55] stringi_1.7.6 MASS_7.3-60 Rtsne_0.16 plyr_1.8.9 grid_4.2.0 parallel_4.2.0
[61] listenv_0.9.0 promises_1.2.1 ggrepel_0.9.3 deldir_1.0-9 miniUI_0.1.1.1 lattice_0.21-9
[67] cowplot_1.1.1 splines_4.2.0 tensor_1.5 pillar_1.9.0 igraph_1.5.1 spatstat.geom_3.2-5
[73] future.apply_1.11.0 reshape2_1.4.4 codetools_0.2-19 leiden_0.4.3 glue_1.6.2 data.table_1.14.8
[79] png_0.1-8 vctrs_0.6.3 httpuv_1.6.11 polyclip_1.10-6 gtable_0.3.4 RANN_2.6.1
[85] purrr_1.0.2 tidyr_1.3.0 scattermore_1.2 future_1.33.0 mime_0.12 xtable_1.8-4
[91] later_1.3.1 survival_3.5-7 viridisLite_0.4.2 tibble_3.2.1 cluster_2.1.4 globals_0.16.2
[97] fitdistrplus_1.1-11 ellipsis_0.3.2 ROCR_1.0-11
Hi there,
When I ran the reliability.test in my own data, I encountered the following error :
May I ask your help for resolving the issue?