* using log directory ‘/srv/hornik/tmp/CRAN_pretest/RCNA.Rcheck’ * using R Under development (unstable) (2024-11-25 r87381) * using platform: x86_64-pc-linux-gnu * R was compiled by Debian clang version 19.1.1 (1) Debian flang-new version 19.1.1 (1) * running under: Debian GNU/Linux trixie/sid * using session charset: UTF-8 * checking for file ‘RCNA/DESCRIPTION’ ... OK * this is package ‘RCNA’ version ‘1.0’ * package encoding: UTF-8 * checking CRAN incoming feasibility ... [3s/3s] NOTE Maintainer: ‘Matt Bradley ’ New submission Possibly misspelled words in DESCRIPTION: CNA (5:80) GC (9:77) NKR (11:60) NKRs (11:6) RCNA (2:49) karyotype (10:62) The Description field should not start with the package name, 'This package' or similar. * 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 ‘RCNA’ can be installed ... [3s/3s] 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 code files for non-ASCII characters ... OK * checking R files for syntax errors ... OK * checking whether the package can be loaded ... [1s/1s] OK * checking whether the package can be loaded with stated dependencies ... [1s/1s] OK * checking whether the package can be unloaded cleanly ... [1s/1s] OK * checking whether the namespace can be loaded with stated dependencies ... [1s/1s] OK * checking whether the namespace can be unloaded cleanly ... [1s/1s] OK * checking loading without being on the library search path ... [1s/1s] 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 ... [5s/5s] OK * checking Rd files ... [0s/0s] OK * checking Rd metadata ... OK * checking Rd line widths ... NOTE Rd file 'create_RCNA_object.Rd': \examples lines wider than 100 characters: file.raw.coverage = system.file("examples", "coverage", paste0(samples, ".txt.gz"), package = "RCNA"), These lines will be truncated in the PDF manual. * 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 ... [1s/1s] OK * checking LazyData ... OK * checking data for ASCII and uncompressed saves ... OK * checking installed files from ‘inst/doc’ ... OK * checking files in ‘vignettes’ ... OK * checking examples ... [1s/1s] ERROR Running examples in ‘RCNA-Ex.R’ failed The error most likely occurred in: > base::assign(".ptime", proc.time(), pos = "CheckExEnv") > ### Name: correct_gc_bias > ### Title: correct_gc_bias: Estimate and correct GC bias in coverage > ### Aliases: correct_gc_bias correct_gc_bias.default > ### correct_gc_bias.RCNA_object > > ### ** Examples > > ## Run GC-bias estimation and correction on example object > # See example in create_RCNA_object for info on example_obj included in package > example_obj An object of class "RCNA_object" Slot "sample.names": [1] "ex-sample-1" "ex-sample-2" "ex-sample-3" Slot "ano.file": [1] "/home/mbradley/R/x86_64-pc-linux-gnu-library/4.2/RCNA/examples/annotations-example.csv" Slot "out.dir": [1] "output" Slot "ncpu": [1] 1 Slot "win.size": [1] 75 Slot "gc.step": [1] 0.01 Slot "estimate_gc": [1] TRUE Slot "nkr": [1] 0.9 Slot "norm.cov.matrix": [1] "output/norm-cov-matrix.csv.gz" Slot "low.score.cutoff": [1] -0.35 Slot "high.score.cutoff": [1] 0.35 Slot "gcParams": file.raw.coverage 1 /home/mbradley/R/x86_64-pc-linux-gnu-library/4.2/RCNA/examples/coverage/ex-sample-1.txt.gz 2 /home/mbradley/R/x86_64-pc-linux-gnu-library/4.2/RCNA/examples/coverage/ex-sample-2.txt.gz 3 /home/mbradley/R/x86_64-pc-linux-gnu-library/4.2/RCNA/examples/coverage/ex-sample-3.txt.gz sample.names file.corrected.coverage 1 ex-sample-1 output/gc/ex-sample-1.corrected.txt.gz 2 ex-sample-2 output/gc/ex-sample-2.corrected.txt.gz 3 ex-sample-3 output/gc/ex-sample-3.corrected.txt.gz Slot "nkrParams": file.nkr.coverage x.norm sample.names 1 output/gc/ex-sample-1.corrected.txt.gz FALSE ex-sample-1 2 output/gc/ex-sample-2.corrected.txt.gz FALSE ex-sample-2 3 output/gc/ex-sample-3.corrected.txt.gz FALSE ex-sample-3 Slot "scoreParams": file.score.coverage sample.names 1 output/gc/ex-sample-1.corrected.txt.gz ex-sample-1 2 output/gc/ex-sample-2.corrected.txt.gz ex-sample-2 3 output/gc/ex-sample-3.corrected.txt.gz ex-sample-3 Slot "commands": list() > dir.create(file.path("output", "gc"), recursive = TRUE) > correct_gc_analysisObj <- correct_gc_bias(example_obj) Error in { : task 1 failed - "cannot open the connection" Calls: correct_gc_bias ... correct_gc_bias.RCNA_object -> %dopar% -> Execution halted * checking for unstated dependencies in vignettes ... OK * checking package vignettes ... OK * checking re-building of vignette outputs ... [1s/1s] OK * checking PDF version of manual ... [3s/3s] OK * checking HTML version of manual ... [0s/0s] OK * checking for non-standard things in the check directory ... NOTE Found the following files/directories: ‘output’ * checking for detritus in the temp directory ... OK * DONE Status: 1 ERROR, 3 NOTEs