* using log directory ‘/srv/hornik/tmp/CRAN_pretest/lrpste.Rcheck’ * using R Under development (unstable) (2026-03-06 r89561) * using platform: x86_64-pc-linux-gnu * R was compiled by Debian clang version 21.1.8 (3+b1) Debian flang version 21.1.8 (3+b1) * running under: Debian GNU/Linux forky/sid * using session charset: UTF-8 * current time: 2026-03-08 00:13:15 UTC * checking for file ‘lrpste/DESCRIPTION’ ... OK * checking extension type ... Package * this is package ‘lrpste’ version ‘1.0’ * package encoding: UTF-8 * checking CRAN incoming feasibility ... [2s/3s] NOTE Maintainer: ‘Chun-Xiao Nie ’ New submission Possibly misspelled words in DESCRIPTION: LRP (3:8, 11:70) The Description field should not start with the package name, 'This package' or similar. * 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 ‘lrpste’ 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 code 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 ... WARNING '::' or ':::' import not declared from: ‘localinfor’ 'library' or 'require' call to ‘RTransferEntropy’ which was already attached by Depends. Please remove these calls from your code. Packages in Depends field not imported from: ‘RTransferEntropy’ ‘doParallel’ ‘foreach’ These packages need to be imported from (in the NAMESPACE file) for when this namespace is loaded but not attached. * checking S3 generic/method consistency ... OK * checking replacement functions ... OK * checking foreign function calls ... OK * checking R code for possible problems ... [2s/2s] NOTE etematrix: no visible global function definition for ‘combn’ etematrix: no visible global function definition for ‘calc_ete’ localte: no visible global function definition for ‘calc_te’ localtematrixnrand: no visible global function definition for ‘%do%’ localtematrixnrand: no visible global function definition for ‘%dopar%’ localtematrixseq: no visible global function definition for ‘sd’ localtematrixseq: no visible global function definition for ‘pnorm’ localteseries: no visible global function definition for ‘calc_te’ localteseries: no visible global function definition for ‘sd’ localteseries: no visible global function definition for ‘pnorm’ telabmatrix: no visible global function definition for ‘calc_te’ tematrix: no visible global function definition for ‘combn’ tematrix: no visible global function definition for ‘calc_te’ tepvaluematrix: no visible global function definition for ‘combn’ tepvector: no visible global function definition for ‘transfer_entropy’ Undefined global functions or variables: %do% %dopar% calc_ete calc_te combn pnorm sd transfer_entropy Consider adding importFrom("stats", "pnorm", "sd") importFrom("utils", "combn") to your NAMESPACE file. * 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 ... WARNING Undocumented code objects: ‘model01’ ‘model02’ ‘stocks’ ‘szpv’ Undocumented data sets: ‘model01’ ‘model02’ ‘stocks’ ‘szpv’ All user-level objects in a package should have documentation entries. See chapter ‘Writing R documentation files’ in the ‘Writing R Extensions’ manual. * checking for code/documentation mismatches ... OK * checking Rd \usage sections ... WARNING Undocumented arguments in Rd file 'localte.Rd' ‘lx’ ‘ly’ Undocumented arguments in Rd file 'localtematrix.Rd' ‘lx’ ‘ly’ Undocumented arguments in Rd file 'localtematrixnrand.Rd' ‘ncores’ Undocumented arguments in Rd file 'localtematrixseq.Rd' ‘ncores’ Undocumented arguments in Rd file 'localtesample.Rd' ‘lx’ ‘ly’ Undocumented arguments in Rd file 'localteseries.Rd' ‘lx’ ‘ly’ Functions with \usage entries need to have the appropriate \alias entries, and all their arguments documented. The \usage entries must correspond to syntactically valid R code. See chapter ‘Writing R documentation files’ in the ‘Writing R Extensions’ manual. * 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 ... [55s/55s] ERROR Running examples in ‘lrpste-Ex.R’ failed The error most likely occurred in: > base::assign(".ptime", proc.time(), pos = "CheckExEnv") > ### Name: localtematrixseq > ### Title: This function implements a matrix version of LRP-based analysis. > ### Aliases: localtematrixseq > > ### ** Examples > > s1=matrix(0,200,6) > s1[,1]=rnorm(200,0,1) > s1[,4]=rnorm(200,0,1) > for (i in 2:200){s1[i,2]=s1[c(i-1),1]^2+rnorm(1,0,0.2) + s1[i,3]=s1[c(i-1),1]^3+rnorm(1,0,0.2) + s1[i,5]=abs(s1[c(i-1),4])+rnorm(1,0,0.2) + s1[i,6]=abs(s1[c(i-1),4])+s1[c(i-1),1]+rnorm(1,0,0.2)} > s=matrix(0,600,6) > s[1:200,]=matrix(data=rnorm(1200,0,1),200,6) > s[201:400,]=s1 > s[401:600,]=matrix(data=rnorm(1200,0,1),200,6) > te=tepvaluematrix(s,1,1,c(25,50,75),100) Shannon's entropy on 1 core with 100 shuffles. x and y have length 600 (0 NAs removed) [calculate] X->Y transfer entropy [calculate] Y->X transfer entropy [bootstrap] 100 times Done - Total time 1.47 seconds Shannon's entropy on 1 core with 100 shuffles. x and y have length 600 (0 NAs removed) [calculate] X->Y transfer entropy [calculate] Y->X transfer entropy [bootstrap] 100 times Done - Total time 1.5 seconds Shannon's entropy on 1 core with 100 shuffles. x and y have length 600 (0 NAs removed) [calculate] X->Y transfer entropy [calculate] Y->X transfer entropy [bootstrap] 100 times Done - Total time 1.47 seconds Shannon's entropy on 1 core with 100 shuffles. x and y have length 600 (0 NAs removed) [calculate] X->Y transfer entropy [calculate] Y->X transfer entropy [bootstrap] 100 times Done - Total time 1.47 seconds Shannon's entropy on 1 core with 100 shuffles. x and y have length 600 (0 NAs removed) [calculate] X->Y transfer entropy [calculate] Y->X transfer entropy [bootstrap] 100 times Done - Total time 1.49 seconds Shannon's entropy on 1 core with 100 shuffles. x and y have length 600 (0 NAs removed) [calculate] X->Y transfer entropy [calculate] Y->X transfer entropy [bootstrap] 100 times Done - Total time 1.49 seconds Shannon's entropy on 1 core with 100 shuffles. x and y have length 600 (0 NAs removed) [calculate] X->Y transfer entropy [calculate] Y->X transfer entropy [bootstrap] 100 times Done - Total time 1.5 seconds Shannon's entropy on 1 core with 100 shuffles. x and y have length 600 (0 NAs removed) [calculate] X->Y transfer entropy [calculate] Y->X transfer entropy [bootstrap] 100 times Done - Total time 1.48 seconds Shannon's entropy on 1 core with 100 shuffles. x and y have length 600 (0 NAs removed) [calculate] X->Y transfer entropy [calculate] Y->X transfer entropy [bootstrap] 100 times Done - Total time 1.48 seconds Shannon's entropy on 1 core with 100 shuffles. x and y have length 600 (0 NAs removed) [calculate] X->Y transfer entropy [calculate] Y->X transfer entropy [bootstrap] 100 times Done - Total time 1.48 seconds Shannon's entropy on 1 core with 100 shuffles. x and y have length 600 (0 NAs removed) [calculate] X->Y transfer entropy [calculate] Y->X transfer entropy [bootstrap] 100 times Done - Total time 1.49 seconds Shannon's entropy on 1 core with 100 shuffles. x and y have length 600 (0 NAs removed) [calculate] X->Y transfer entropy [calculate] Y->X transfer entropy [bootstrap] 100 times Done - Total time 1.49 seconds Shannon's entropy on 1 core with 100 shuffles. x and y have length 600 (0 NAs removed) [calculate] X->Y transfer entropy [calculate] Y->X transfer entropy [bootstrap] 100 times Done - Total time 1.47 seconds Shannon's entropy on 1 core with 100 shuffles. x and y have length 600 (0 NAs removed) [calculate] X->Y transfer entropy [calculate] Y->X transfer entropy [bootstrap] 100 times Done - Total time 1.52 seconds Shannon's entropy on 1 core with 100 shuffles. x and y have length 600 (0 NAs removed) [calculate] X->Y transfer entropy [calculate] Y->X transfer entropy [bootstrap] 100 times Done - Total time 1.47 seconds > adj=pmatrixtonetwork(te$tep,0.05) > lab=which(adj>0,arr.ind = TRUE) > teseq=localtematrixseq(s,100,10,1,1,c(25,50,75),60,lab,2) Error in checkForRemoteErrors(lapply(cl, recvResult)) : 2 nodes produced errors; first error: there is no package called ‘localinfor’ Calls: localtematrixseq ... localtematrixnrand -> -> clusterCall -> checkForRemoteErrors Execution halted Examples with CPU (user + system) or elapsed time > 5s user system elapsed localtematrix 22.385 0.000 22.399 etematrix 9.885 0.012 9.903 * 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, 3 WARNINGs, 2 NOTEs