Error in reliability.test

[Liux0228]

Hi there,

When I ran the reliability.test in my own data, I encountered the following error :

result2 <- reliability.test(X, Y, network, alpha = 0.05, family = "binomial", cell_nu+ = numbers, n = 2, nfold = 5
+ )
[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 ...

May I ask your help for resolving the issue?

[Liux0228]

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