* using log directory ‘/data/gannet/ripley/R/packages/tests-LENGTH1/nos.Rcheck’
* using R Under development (unstable) (2022-04-26 r82260)
* using platform: x86_64-pc-linux-gnu (64-bit)
* using session charset: UTF-8
* using option ‘--no-stop-on-test-error’
* checking for file ‘nos/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘nos’ version ‘1.1.0’
* package encoding: UTF-8
* 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 whether package ‘nos’ can be installed ... [8s/22s] OK
* checking package directory ... 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 ... [12s/31s] 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 ... [15s/52s] ERROR
Running examples in ‘nos-Ex.R’ failed
The error most likely occurred in:

> ### Name: NOSM_POT_dir
> ### Title: Compute NOS using a directed network and with a user provided
> ###   network of potential interactions
> ### Aliases: NOSM_POT_dir
> 
> ### ** Examples
> 
> data(boreal)
> y <-  boreal[1:300,] #subset 300 rows for speed
> d <- sample(nrow(y), 200, replace = FALSE) #create a random pot_net
> pot_net <- y[d,] #by randomly sampling 200 rows from boreal
> x <- NOSM_POT_dir(y, pot_net, perc = 1, sl = 1)
 ----------- FAILURE REPORT -------------- 
 --- failure: length > 1 in coercion to logical ---
 --- srcref --- 
: 
 --- package (from environment) --- 
nos
 --- call from context --- 
OV(x$adj_in, x$pot_in, perc, sl)
 --- call from argument --- 
j > i && LL[[i]] > 0
 --- R stacktrace ---
where 1: OV(x$adj_in, x$pot_in, perc, sl)
where 2: NOSM_POT_dir(y, pot_net, perc = 1, sl = 1)

 --- value of length: 2 type: logical ---
[1] TRUE TRUE
 --- function from context --- 
function (LL, LL_pot, perc = 1, sl = 1) 
{
    CO <- c()
    for (i in 1:length(LL)) {
        for (j in 1:length(LL)) {
            if (perc == 1 || ((runif(1)) < perc)) {
                if (j > i && LL[[i]] > 0 && LL[[j]] > 0) {
                  pot <- intersect(LL_pot[[i]], LL_pot[[j]])
                  if (sl == 1) {
                    if (i %in% pot) 
                      pot <- pot[-which(pot == i)]
                    if (j %in% pot) 
                      pot <- pot[-which(pot == j)]
                  }
                  N <- length(pot)
                  rr1 <- intersect(LL[[i]], pot)
                  rr2 <- intersect(LL[[j]], pot)
                  N1 <- length(rr1)
                  N2 <- length(rr2)
                  S <- length(intersect(rr1, rr2))
                  co <- 0
                  for (k in seq(0, (min(N1, N2)))) {
                    ccc <- cooc(k, N, N1, N2)
                    co <- co + (ccc * k)
                  }
                  if (co != min(N1, N2)) {
                    if (S >= co) {
                      score <- (S - co)/(min(N1, N2) - co)
                    }
                    else {
                      if ((N1 + N2 - N) < 0) {
                        score <- (S - co)/co
                      }
                      else {
                        score <- (S - co)/(co - (min(N1, N2) - 
                          (N - max(N1, N2))))
                      }
                    }
                    CO <- c(CO, score)
                  }
                  else {
                    CO <- c(CO, 1)
                  }
                }
            }
        }
    }
    return(CO)
}
<bytecode: 0x69063f8>
<environment: namespace:nos>
 --- function search by body ---
Function OV in namespace nos has this body.
 ----------- END OF FAILURE REPORT -------------- 
Fatal error: length > 1 in coercion to logical
* checking PDF version of manual ... OK
* checking for non-standard things in the check directory ... OK
* checking for detritus in the temp directory ... OK
* DONE

Status: 1 ERROR
See
  ‘/data/gannet/ripley/R/packages/tests-LENGTH1/nos.Rcheck/00check.log’
for details.

Command exited with non-zero status 1
Time 3:58.05, 73.49 + 8.70