* using log directory 'd:/Rcompile/CRANpkg/local/4.6/rnaCrosslinkOO.Rcheck'
* using R Under development (unstable) (2025-07-21 r88439 ucrt)
* using platform: x86_64-w64-mingw32
* R was compiled by
    gcc.exe (GCC) 14.2.0
    GNU Fortran (GCC) 14.2.0
* running under: Windows Server 2022 x64 (build 20348)
* using session charset: UTF-8
* checking for file 'rnaCrosslinkOO/DESCRIPTION' ... OK
* checking extension type ... Package
* this is package 'rnaCrosslinkOO' version '0.1.4'
* 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 hidden files and directories ... OK
* checking for portable file names ... OK
* checking whether package 'rnaCrosslinkOO' can be installed ... OK
* checking installed package size ... OK
* checking package directory ... OK
* checking 'build' 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 code files for non-ASCII characters ... OK
* checking R files for syntax errors ... OK
* checking whether the package can be loaded ... [7s] OK
* checking whether the package can be loaded with stated dependencies ... [8s] OK
* checking whether the package can be unloaded cleanly ... [8s] OK
* checking whether the namespace can be loaded with stated dependencies ... [7s] OK
* checking whether the namespace can be unloaded cleanly ... [7s] OK
* checking loading without being on the library search path ... [8s] 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 ... [21s] OK
* checking Rd files ... [1s] OK
* checking Rd metadata ... 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 installed files from 'inst/doc' ... OK
* checking files in 'vignettes' ... OK
* checking examples ... [33s] ERROR
Running examples in 'rnaCrosslinkOO-Ex.R' failed
The error most likely occurred in:

> ### Name: plotClusterAgreementHeat
> ### Title: Plot a heatmap that plots the agreements between replicates
> ###   after clusterrnaCrosslink has been performed
> ### Aliases: plotClusterAgreementHeat
> ###   plotClusterAgreementHeat,rnaCrosslinkDataSet-method
> 
> ### ** Examples
> 
> 
> cds = makeExamplernaCrosslinkDataSet()
 ******************************************** 
 *****            rnaCrosslink-OO          ****** 
 ******************************************** 
 *****-------*******************-------****** 
 *****       Reading SampleTable       ****** 
 *****       Detected  2  Samples      ****** 
 *****     detected group c:: 2       ***** 
 *****     detected group s:: 1       ***** 
 ****      Sample Names:  s1 c1    ****  ****      Sample Names:  s1 c1    ****  ****      Sample Names:  s1 c1    ****  ****      Sample Names:  s1 c1    **** 
 *****         Reading Input Files        ***** 
 *****  Checking Subsetting Options  ***** 
 *****  No user subsetting chosen  ***** 
 *****  Checking Sampling Options  ***** 
 *****  No user sampling chosen  ***** 
 *****     Getting RNAs of Interest    ****** 
 *****    RNA of interest + Host RNA    ***** 
 *****      RNA of interest Alone       ***** 
 *****         Making Matrices         ****** 
 *****          RNA Size:  83         ***** 
 *****         Creating object          ***** 
 *****-------*******************-------****** 
 ******************************************** 
 ******************************************** 
> 
> 
> clusteredCds = clusterrnaCrosslink(cds,
+                 cores = 1,
+                 stepCount = 1,
+                 clusterCutoff = 0)
********************************************
****  transcript1  *****
****               83  nt             ****
****       Assessing Long Range         ****
****        Sampling Long Range         ****
Error in serverSocket(port = port) : 
  creation of server socket failed: port 11668 cannot be opened
Calls: clusterrnaCrosslink ... clusterrnaCrosslink -> makeCluster -> makePSOCKcluster -> serverSocket
Execution halted
* checking for unstated dependencies in 'tests' ... OK
* checking tests ... [8s] OK
  Running 'testthat.R' [8s]
* checking for unstated dependencies in vignettes ... OK
* checking package vignettes ... OK
* checking re-building of vignette outputs ... [309s] OK
* checking PDF version of manual ... [22s] OK
* checking HTML version of manual ... [8s] OK
* DONE
Status: 1 ERROR