* using log directory 'd:/RCompile/CRANincoming/R-devel/rnaCrosslinkOO.Rcheck'
* using R Under development (unstable) (2024-02-21 r85967 ucrt)
* using platform: x86_64-w64-mingw32
* R was compiled by
    gcc.exe (GCC) 12.3.0
    GNU Fortran (GCC) 12.3.0
* 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 '0.1.2'
* package encoding: UTF-8
* checking CRAN incoming feasibility ... NOTE
Maintainer: 'Jonathan Price <jlp76@cam.ac.uk>'

New submission

Possibly misspelled words in DESCRIPTION:
  Crosslinking (3:24)
  crosslinking (14:30)
* 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 serialization versions ... OK
* checking whether package 'rnaCrosslinkOO' can be installed ... OK
* checking installed package size ... OK
* checking package directory ... OK
* checking for future file timestamps ... 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 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 ... [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 installed files from 'inst/doc' ... OK
* checking files in 'vignettes' ... OK
* checking examples ... [24s] ERROR
Running examples in 'rnaCrosslinkOO-Ex.R' failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: plotClusterAgreement
> ### Title: Plot a heatmap that plots the agreements between replicates
> ###   after clusterrnaCrosslink has been performed
> ### Aliases: plotClusterAgreement
> ###   plotClusterAgreement,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        ***** 
 *****     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         ****
****      Assessing Short Range         ****
****      Sampling short Range          ****
*****        done  s1 1  / 1           *****
*****        done  c1 1  / 1           *****
*****          Creating object         *****
******************************************** 
> 
> 
> plotClusterAgreement(cds)
Error in matrix(0, nrow = nrow(getData(cds, "matrixList", analysisStage)[[samples[1]]]),  : 
  non-numeric matrix extent
Calls: plotClusterAgreement -> plotClusterAgreement -> matrix
Execution halted
* checking for unstated dependencies in 'tests' ... OK
* checking tests ... OK
  Running 'testthat.R'
* checking for unstated dependencies in vignettes ... OK
* checking package vignettes ... OK
* checking re-building of vignette outputs ... [329s] OK
* checking PDF version of manual ... [13s] OK
* checking HTML version of manual ... OK
* DONE
Status: 1 ERROR, 1 NOTE