* using log directory ‘/data/blackswan/ripley/R/packages/tests-devel/kmeRtone.Rcheck’
* using R Under development (unstable) (2026-01-14 r89303)
* 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 ‘kmeRtone/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘kmeRtone’ version ‘1.0’
* 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 ‘kmeRtone’ can be installed ... [84s/78s] OK
* used C++ compiler: ‘g++ (GCC) 14.2.1 20240912 (Red Hat 14.2.1-3)’
* 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 whether startup messages can be suppressed ... 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 ... [24s/24s] 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 LazyData ... OK
* checking data for ASCII and uncompressed saves ... OK
* checking line endings in C/C++/Fortran sources/headers ... OK
* checking line endings in Makefiles ... OK
* checking compilation flags in Makevars ... OK
* checking for GNU extensions in Makefiles ... INFO
GNU make is a SystemRequirements.
* checking for portable use of $(BLAS_LIBS) and $(LAPACK_LIBS) ... OK
* checking use of PKG_*FLAGS in Makefiles ... OK
* checking use of SHLIB_OPENMP_*FLAGS in Makefiles ... OK
* checking compilation flags used ... OK
* checking compiled code ... OK
* checking sizes of PDF files under ‘inst/doc’ ... OK
* checking installed files from ‘inst/doc’ ... OK
* checking examples ... OK
* checking examples with --run-donttest ... [15s/24s] ERROR
Running examples in ‘kmeRtone-Ex.R’ failed
The error most likely occurred in:

> ### Name: example_kmeRtone_score
> ### Title: Example 2-mer enrichment/depletion scores
> ### Aliases: example_kmeRtone_score
> ### Keywords: datasets
> 
> ### ** Examples
> 
> ## No test: 
> # 1. Randomly generate genomic positions and save results
> library(data.table)

Attaching package: ‘data.table’

The following object is masked from ‘package:base’:

    %notin%

> library(kmeRtone)
> temp_dir <- tempdir()
> 
> set.seed(1234)
> temp_files <- character(1)
> for(chr in 1){
+     genomic_coor <- data.table(
+         seqnames = paste0("chr", chr),
+         start = sample(
+             x = 10000:10000000, 
+             size = 100000, 
+             replace = FALSE
+         ),
+         width = 2
+     )
+ 
+     f <- file.path(temp_dir, paste0("chr", chr, ".csv"))
+     fwrite(genomic_coor, f)
+     temp_files[chr] <- f
+ }
> 
> # 2. Run kmeRtone score function
> temp_dir_genome <- tempdir()
> kmeRtone::kmeRtone(
+     case.coor.path = temp_dir, 
+     genome.name = "hg19", 
+     genome.path = temp_dir_genome,
+     strand.sensitive = FALSE, 
+     k = 2,
+     ctrl.rel.pos = c(80, 500),
+     case.pattern = NULL,
+     single.case.len = 2,
+     output.dir = temp_dir,
+     module = "score",
+     rm.case.kmer.overlaps = FALSE,
+     merge.replicate = TRUE, 
+     kmer.table = NULL,
+     verbose = TRUE
+ )


------------------------------------------------------------
                 Extraction of Case K-mers                 
------------------------------------------------------------
  % Total    % Received % Xferd  Average Speed   Time    Time     Time  Current
                                 Dload  Upload   Total   Spent    Left  Speed

  0     0    0     0    0     0      0      0 --:--:-- --:--:-- --:--:--     0
  0     0    0     0    0     0      0      0 --:--:-- --:--:-- --:--:--     0
  1 70.3M    1  929k    0     0   690k      0  0:01:44  0:00:01  0:01:43  690k
 16 70.3M   16 11.3M    0     0  4859k      0  0:00:14  0:00:02  0:00:12 4859k
 30 70.3M   30 21.5M    0     0  6439k      0  0:00:11  0:00:03  0:00:08 6438k
 45 70.3M   45 32.3M    0     0  7618k      0  0:00:09  0:00:04  0:00:05 7618k
 59 70.3M   59 42.0M    0     0  8030k      0  0:00:08  0:00:05  0:00:03 8772k
 76 70.3M   76 53.5M    0     0  8620k      0  0:00:08  0:00:06  0:00:02 10.4M
 92 70.3M   92 65.2M    0     0  9075k      0  0:00:07  0:00:07 --:--:-- 10.8M
100 70.3M  100 70.3M    0     0  9133k      0  0:00:07  0:00:07 --:--:-- 10.9M
Extracting 2-mers from chr1.............DONE! -- 14.56 secs

Downloading chr1.fa.gz from UCSC...


Total time taken: 16.44 secs 
------------------------------------------------------------
                Extraction of Control K-mers                
------------------------------------------------------------
Building control regions of chr1........DONE! -- 0.47 secs

Total time taken: 1.65 secs 
Error in getGlobalsAndPackages(expr, envir = envir, globals = globals) : 
  The total size of the 44 globals exported for future expression (‘FUN()’) is 951.26 MiB. This exceeds the maximum allowed size 500.00 MiB per by R option "future.globals.maxSize". This limit is set to protect against transfering too large objects to parallel workers by mistake, which may not be intended and could be costly. See help("future.globals.maxSize", package = "future") for further explainations and how to adjust or remove this threshold The three largest globals are ‘FUN’ (237.80 MiB of class ‘function’), ‘initialize.kmer.table’ (237.77 MiB of class ‘function’) and ‘map.kmers’ (237.77 MiB of class ‘function’)
Calls: <Anonymous> ... getGlobalsAndPackagesXApply -> getGlobalsAndPackages
Execution halted
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
  Running ‘testthat.R’ [20s/31s]
 [21s/31s] OK
* 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/kmeRtone.Rcheck/00check.log’
for details.

Command exited with non-zero status 1
Time 4:21.21, 208.72 + 38.93