* using log directory ‘/data/blackswan/ripley/R/packages/tests-devel/OpEnCAST.Rcheck’
* using R Under development (unstable) (2026-01-29 r89353)
* using platform: x86_64-pc-linux-gnu
* R was compiled by
    gcc (GCC) 14.2.1 20240912 (Red Hat 14.2.1-3)
    GNU Fortran (GCC) 14.2.1 20240912 (Red Hat 14.2.1-3)
* running under: Fedora Linux 40 (Workstation Edition)
* using session charset: UTF-8
* checking for file ‘OpEnCAST/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘OpEnCAST’ version ‘0.1.1’
* 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 ‘OpEnCAST’ can be installed ... [12s/12s] 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 code 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 ... [18s/18s] 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 examples ... OK
* checking examples with --run-donttest ... [68s/422s] ERROR
Running examples in ‘OpEnCAST-Ex.R’ failed
The error most likely occurred in:

> ### Name: Dicot_MethPred
> ### Title: DNA Methylation Prediction in Dicot Plants
> ### Aliases: Dicot_MethPred
> 
> ### ** Examples
> 
> ## No test: 
> library(OpEnCAST)
> data<-system.file("exdata/test.fasta", package = "OpEnCAST")
> pred<-Dicot_MethPred(fasta_file_path=data, Reference="Arabidopsis")
Warning in readLines(file) :
  incomplete final line found on '/data/blackswan/ripley/R/packages/tests-devel/OpEnCAST.Rcheck/OpEnCAST/exdata/test.fasta'
Warning in readLines(file) :
  incomplete final line found on '/data/blackswan/ripley/R/packages/tests-devel/OpEnCAST.Rcheck/OpEnCAST/exdata/test.fasta'
The sequences ( Positive_4mC_26370, Positive_4mC_35265, Positive_4mC_35266, Positive_4mC_35267, Positive_4mC_50891, Positive_4mC_55948, Positive_4mC_55949, Positive_4mC_64559, Positive_4mC_64562, Positive_4mC_70963, Positive_4mC_81155, Positive_4mC_81253, Positive_4mC_81907, Positive_4mC_89569, Positive_4mC_90330, Positive_4mC_90331, Positive_4mC_104747, Positive_6mA_37833, Positive_6mA_37834, Positive_6mA_37861, Positive_6mA_39153, Positive_6mA_39154, Positive_6mA_39155, Positive_6mA_39156, Positive_6mA_39157, Positive_6mA_39293, Positive_6mA_39294, Positive_6mA_39295, Positive_6mA_39296, Positive_6mA_39602, Positive_6mA_39603, Positive_6mA_39604, Positive_6mA_39605, Positive_6mA_39606, Positive_6mA_39607, Positive_6mA_39671, Positive_6mA_39672, Positive_6mA_39673, Positive_6mA_39674, Positive_6mA_39675, Positive_6mA_42558, Positive_6mA_43632, Positive_6mA_46693, Positive_6mA_47009, Positive_6mA_51758, Positive_6mA_56382, Positive_6mA_56383 ) were deleted. They contained non-standard alphabets
The sequences ( Negative_4718, Negative_9573, Negative_22707, Negative_23911, Negative_24925, Negative_38899, Negative_44139, Negative_81262, Negative_86511, Negative_87248, Negative_99073, Negative_101693, Negative_105756, Negative_115760, Negative_126258, Negative_128440, Negative_137395, Negative_147067, Negative_147996, Negative_152470, Negative_153668, Negative_160894, Negative_170840, Negative_170841, Negative_170842, Negative_170843 ) were deleted. They contained non-standard alphabets
Warning in readLines(filename) :
  incomplete final line found on '/data/blackswan/ripley/R/packages/tests-devel/OpEnCAST.Rcheck/OpEnCAST/exdata/test.fasta'
Warning in readLines(file) :
  incomplete final line found on '/data/blackswan/ripley/R/packages/tests-devel/OpEnCAST.Rcheck/OpEnCAST/exdata/test.fasta'
Warning in readLines(filename) :
  incomplete final line found on '/data/blackswan/ripley/R/packages/tests-devel/OpEnCAST.Rcheck/OpEnCAST/exdata/test.fasta'
Error in xgb.get.handle(object) : 
  'xgb.Booster' object is corrupted or is from an incompatible XGBoost version.
Calls: Dicot_MethPred ... predict.xgb.Booster -> xgb.best_iteration -> xgb.attr -> xgb.get.handle
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/OpEnCAST.Rcheck/00check.log’
for details.

Command exited with non-zero status 1
Time 9:06.61, 155.77 + 35.80