* using log directory 'd:/RCompile/CRANincoming/R-devel/ExprNet.Rcheck'
* using R Under development (unstable) (2023-09-11 r85126 ucrt)
* using platform: x86_64-w64-mingw32
* R was compiled by
    gcc.exe (GCC) 12.2.0
    GNU Fortran (GCC) 12.2.0
* running under: Windows Server 2022 x64 (build 20348)
* using session charset: UTF-8
* checking for file 'ExprNet/DESCRIPTION' ... OK
* checking extension type ... Package
* this is package 'ExprNet' version '1.1.0'
* package encoding: UTF-8
* checking CRAN incoming feasibility ... Note_to_CRAN_maintainers
Maintainer: 'Wenbin Wu <drkwu999@gmail.com>'
* checking package namespace information ... OK
* checking package dependencies ... OK
* checking if this is a source package ... OK
* checking if there is a namespace ... OK
* checking for hidden files and directories ... OK
* checking for portable file names ... OK
* checking serialization versions ... OK
* checking whether package 'ExprNet' can be installed ... OK
* checking installed package size ... OK
* checking package directory ... OK
* checking for future file timestamps ... OK
* checking DESCRIPTION meta-information ... OK
* checking top-level files ... OK
* checking for left-over files ... OK
* checking index information ... OK
* checking package subdirectories ... OK
* checking R files for non-ASCII characters ... OK
* checking R files for syntax errors ... OK
* checking whether the package can be loaded ... OK
* checking whether the package can be loaded with stated dependencies ... OK
* checking whether the package can be unloaded cleanly ... OK
* checking whether the namespace can be loaded with stated dependencies ... OK
* checking whether the namespace can be unloaded cleanly ... OK
* checking loading without being on the library search path ... OK
* checking use of S3 registration ... OK
* checking dependencies in R code ... OK
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... OK
* checking Rd files ... OK
* checking Rd metadata ... OK
* checking Rd line widths ... OK
* checking Rd cross-references ... OK
* checking for missing documentation entries ... OK
* checking for code/documentation mismatches ... OK
* checking Rd \usage sections ... OK
* checking Rd contents ... OK
* checking for unstated dependencies in examples ... OK
* checking contents of 'data' directory ... OK
* checking data for non-ASCII characters ... OK
* checking LazyData ... OK
* checking data for ASCII and uncompressed saves ... OK
* checking examples ... ERROR
Running examples in 'ExprNet-Ex.R' failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: analysis_ExprNet
> ### Title: Computing and testing AT1 and AT2, and plotting sub-network
> ### Aliases: analysis_ExprNet
> 
> ### ** Examples
> 
> library(ExprNet)
> network <- network_demo
> data_type1 <- data_LGG_demo
> data_type2 <- data_GBM_demo
> edge_pair_selected <- c("1-8", "1-15", "2-16", "3-16", "5-10",
+                         "5-16", "8-11", "8-13", "8-14", "8-15", "13-15")
> # compute AT's
> AT_res <- analysis_ExprNet(data_type1 = data_type1, data_type2 = data_type2, network = network,
+                            edge_pair_selected = edge_pair_selected,
+                            AT2_perm_test = TRUE, num_perm = 250, num_cores = 2,
+                            type1_name = "LGG", type2_name = "GBM",
+                            subnet_label = "Demo_GO0006306_DNA_methylation(LGG-GBM)",
+                            vertex.label.cex = 1, vertex.size = 10, edge.width = 7)
This graph was created by an old(er) igraph version.
  Call upgrade_graph() on it to use with the current igraph version
  For now we convert it on the fly...

Data read successfully.
17 features
5 samples for phenotype 1
5 samples for phenotype 2.

Graph imported successfully.
There are 17 vertices and 17 edges in the graph.

---Computing edge length and t statistics---
3 / 17 Edges Computed
6 / 17 Edges Computed
10 / 17 Edges Computed
13 / 17 Edges Computed
17 / 17 Edges Computed

Among 17 edge distances, 
4 of them have significant differences at 0.05 level.
5 of them > 0.
12 of them < 0.


The subnetwork consists of 11 edges.


---Computing AT1---

AT1 = 0.67, pval_AT1 = 0.0529


---Computing AT2---

The permutation test may take some time, especially for high dimension. Please stay tuned.

Parallel Computing: 2 cores registered.

Error in { : task 1 failed - "cannot use 'paired' in formula method"
Calls: analysis_ExprNet -> compute_AT -> %dopar% -> <Anonymous>
Execution halted
* checking for unstated dependencies in 'tests' ... OK
* checking tests ... OK
  Running 'testthat.R'
* checking PDF version of manual ... [14s] OK
* checking HTML version of manual ... OK
* DONE
Status: 1 ERROR