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I am running the R CMD check --as-cran option to check a package which I am writing before the submission to CRAN. The tests on MAC and Linux seems to be ok. However, checking the package on Windows returns me an ERROR (below). I already tried to close possible cluster left open by the packages parallel and doParallel. This error only happen when I use the flag --as-cran. If I run the check without it, the process run without errors.

Running examples in 'package1-Ex.R' failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: find_genes_qtls_around_markers
> ### Title: Search genes and QTLs around candidate regions
> ### Aliases: find_genes_qtls_around_markers
> 
> ### ** Examples
> 
> data(QTLmarkers)
> data(gffQTLs)
> out.qtls<-find_genes_qtls_around_markers(db_file=gffQTLs,
+ marker_file=QTLmarkers, method = "qtl",
+ marker = "snp", interval = 500000, nThreads = 2)
You are using the method: qtl with snp

Starting QTL searching using 5e+05 bp as interval

Preparing output file for QTL annotation

> 
> 
> 
> base::assign(".dptime", (proc.time() - get(".ptime", pos = "CheckExEnv")), pos = "CheckExEnv")
> base::cat("find_genes_qtls_around_markers", base::get(".format_ptime", pos = 'CheckExEnv')(get(".dptime", pos = "CheckExEnv")), "\n", file=base::get(".ExTimings", pos = 'CheckExEnv'), append=TRUE, sep="\t")
> cleanEx()
Error: connections left open:
    <-DESKTOP-9GJBKTN:11235 (sockconn)
    <-DESKTOP-9GJBKTN:11235 (sockconn)
Execution halted```
Martijn Pieters
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Pablo Fonseca
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  • How are you using parallel? Is this thread any use to you? https://stackoverflow.com/a/9518950/12957340 – jared_mamrot Jul 28 '20 at 05:43
  • Hello @jared_mamrot. Yes, I am using parallel. It doesn't seems to be any problem with zombie processes once the check occurs without errors removing the --as-cran flag and the functions work perfectly in all the testes systems. It is seems some bug from this specific check. What I did to solve my problem was edit my code to allow sequential analysis as well and run the exampled for the R function sequentially. – Pablo Fonseca Jul 28 '20 at 18:42

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