• 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
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• checking whether package 'rnaCrosslinkOO' can be installed ... OK See the install log for details.
• checking installed package size ... OK
• checking package directory ... OK
• checking 'build' directory ... OK
• checking DESCRIPTION meta-information ... OK
• checking top-level files ... OK
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• 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
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• checking R code for possible problems ... [21s] OK
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• 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