* using log directory ‘/data/blackswan/ripley/R/packages/tests-devel/iCAMP.Rcheck’
* using R Under development (unstable) (2022-04-17 r82203)
* using platform: x86_64-pc-linux-gnu (64-bit)
* using session charset: UTF-8
* checking for file ‘iCAMP/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘iCAMP’ version ‘1.3.4’
* 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 ‘iCAMP’ can be installed ... [11s/11s] 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 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 ... [23s/23s] 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 data for ASCII and uncompressed saves ... OK
* checking examples ... [14s/28s] OK
* checking examples with --run-donttest ... [6s/20s] ERROR
Running examples in ‘iCAMP-Ex.R’ failed
The error most likely occurred in:

> ### Name: bNRI.bin.big
> ### Title: Calculate beta net relatedness index (betaNRI) for each
> ###   phylogenetic bin
> ### Aliases: bNRI.bin.big
> ### Keywords: phylogenetic
> 
> ### ** Examples
> 
> # this function is usually used in icamp.big when setting phylo.rand.scale="across",
> # means randomization across all bins in phylogenetic null model.
> data("example.data")
> comm=example.data$comm
> tree=example.data$tree
> pdid.bin=example.data$pdid.bin
> sp.bin=example.data$sp.bin
> 
> # since pdist.big need to save output to a certain folder,
> # the following code is set as 'not test'.
> # but you may test the example on your computer after change the path for 'save.wd'.
> 
> ## No test: 
> save.wd=tempdir() # please change to the folder you want to save the pd.big output.
> nworker=2 # parallel computing thread number
> pd.big=pdist.big(tree = tree, wd=save.wd, nworker = nworker)
Setting parallel cluster for path computing cost 0.1981647 secs.  Sun Apr 17 23:34:28 2022
Parallel for 10 tips cost 1.454129 secs. Sun Apr 17 23:34:30 2022
Path computing by parallel may take 0.000909274750285678 hours. Sun Apr 17 23:34:30 2022
Now computing path for the rest 20 tips. begin at Sun Apr 17 23:34:30 2022. Please wait...
Computing path for the rest 20 tips actually took 1.760422 secs. Sun Apr 17 23:34:32 2022
Now setting big matrix file on the disk. Sun Apr 17 23:34:32 2022
Setting parallel cluster for pdist computing cost 0.197242 secs.  Sun Apr 17 23:34:32 2022
Parallel computing Pdist for the first 10 runs cost 1.393824 secs. Sun Apr 17 23:34:33 2022
The rest Pdist computing by parallel may take 0.000282819072405497 hours. Sun Apr 17 23:34:33 2022
Computing pdist for the rest 20 tips actually took 1.757155 secs. Sun Apr 17 23:34:35 2022
> rand.time=20 # usually use 1000 for real data.
> 
> bNRIbins=bNRI.bin.big(comm=comm, pd.desc=pd.big$pd.file, pd.spname=pd.big$tip.label,
+                       pd.wd=pd.big$pd.wd, pdid.bin=pdid.bin, sp.bin=sp.bin,
+                       spname.check = FALSE, nworker = nworker, memo.size.GB = 50,
+                       weighted = TRUE, rand = rand.time, output.bMPD = FALSE,
+                       sig.index="SES",unit.sum = NULL, correct.special = TRUE,
+                       detail.null=FALSE, special.method="MPD")
Now calculating observed betaMPD. Begin at Sun Apr 17 23:34:35 2022. Please wait...
Now randomizing by parallel computing. Begin at Sun Apr 17 23:34:36 2022. Please wait...
Error in checkForRemoteErrors(val) : 
  2 nodes produced errors; first error: error in evaluating the argument 'obj' in selecting a method for function 'attach.resource': cannot open the connection
Calls: bNRI.bin.big ... clusterApply -> staticClusterApply -> checkForRemoteErrors
Execution halted
* checking PDF version of manual ... OK
* checking for non-standard things in the check directory ... OK
* checking for detritus in the temp directory ... OK
* checking for new files in some other directories ... OK
* DONE

Status: 1 ERROR
See
  ‘/data/blackswan/ripley/R/packages/tests-devel/iCAMP.Rcheck/00check.log’
for details.

Command exited with non-zero status 1
Time 2:02.66, 86.70 + 7.26