* using log directory ‘/srv/hornik/tmp/CRAN/ExprNet.Rcheck’ * using R Under development (unstable) (2023-09-11 r85126) * using platform: x86_64-pc-linux-gnu * R was compiled by Debian clang version 16.0.6 (11) GNU Fortran (Debian 13.2.0-2) 13.2.0 * running under: Debian GNU/Linux trixie/sid * 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 ... [3s/4s] Note_to_CRAN_maintainers Maintainer: ‘Wenbin Wu ’ * 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 executable files ... OK * checking for hidden files and directories ... OK * checking for portable file names ... OK * checking for sufficient/correct file permissions ... OK * checking serialization versions ... OK * checking whether package ‘ExprNet’ can be installed ... [1s/1s] 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 ... [0s/0s] OK * checking whether the package can be loaded with stated dependencies ... [0s/0s] OK * checking whether the package can be unloaded cleanly ... [0s/0s] OK * checking whether the namespace can be loaded with stated dependencies ... [0s/0s] OK * checking whether the namespace can be unloaded cleanly ... [0s/0s] OK * checking loading without being on the library search path ... [0s/0s] 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 ... [2s/2s] OK * checking Rd files ... [0s/0s] 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 ... [0s/0s] OK * checking LazyData ... OK * checking data for ASCII and uncompressed saves ... OK * checking examples ... [0s/0s] 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% -> Execution halted * checking for unstated dependencies in ‘tests’ ... OK * checking tests ... [1s/1s] OK Running ‘testthat.R’ [1s/1s] * checking PDF version of manual ... [2s/2s] OK * checking HTML version of manual ... [0s/0s] OK * checking for non-standard things in the check directory ... OK * checking for detritus in the temp directory ... OK * DONE Status: 1 ERROR