Biostrings: read*StringSet() functions leave open file handles
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@gerhard-thallinger-1552
Last seen 4 months ago
Austria

When a file is read with any of the read*StringSet() functions, file handles are not closed. This prevents further operations on the file (e.g. deletion).

library(Biostrings)

fsource <- system.file(package="Biostrings", "extdata", "someORF.fa")
fdest <- basename(fsource)
file.copy(fsource, fdest, overwrite=TRUE)
# [1] TRUE
fseq <- readDNAStringSet(fdest)
file.remove(fdest)
# [1] FALSE
# Warning message:
# In file.remove(fdest) :
#   cannot remove file 'someORF.fa', reason 'Permission denied'

Checking for open file handles results in the following:

Rgui.exe           pid: 23312  type: File           384: C:\Users\xxx\Documents\someORF.fa
Rgui.exe           pid: 23312  type: File           38C: C:\Users\xxx\Documents\someORF.fa

Through invoking gc(), the open file handles are closed and the file can be deleted.

gc()
#          used  (Mb) gc trigger  (Mb) max used  (Mb)
# Ncells 2522803 134.8    5198228 277.7  2730967 145.9
# Vcells 4427580  33.8   10146329  77.5  6352280  48.5
file.remove(fdest)
# [1] TRUE

It would be helpful if this could be corrected in the upcoming Bioconductor release.


Environment:


R version 4.3.3 (2024-02-29 ucrt)
Platform: x86_64-w64-mingw32/x64 (64-bit)
Running under: Windows 11 x64 (build 22631)

locale:
[1] LC_COLLATE=English_Austria.utf8  LC_CTYPE=English_Austria.utf8   
[3] LC_MONETARY=English_Austria.utf8 LC_NUMERIC=C                    
[5] LC_TIME=English_Austria.utf8    

time zone: Europe/Vienna
tzcode source: internal

attached base packages:
[1] stats4    stats     graphics  grDevices utils     datasets  methods   base     

other attached packages:
[1] Biostrings_2.70.2   GenomeInfoDb_1.38.6 XVector_0.42.0      IRanges_2.36.0     
[5] S4Vectors_0.40.2    BiocGenerics_0.48.1

loaded via a namespace (and not attached):
[1] zlibbioc_1.48.0         compiler_4.3.3          tools_4.3.3            
[4] GenomeInfoDbData_1.2.11 RCurl_1.98-1.14         crayon_1.5.2           
[7] bitops_1.0-7
Biostrings • 578 views
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Confirmed on windows. Not observed on my linux instance. In other words, the removal succeeds on linux.

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@herve-pages-1542
Last seen 5 hours ago
Seattle, WA, United States

Thanks for the report.

This should be addressed in Biostrings 2.70.3 (BioC 3.18) and Biostrings 2.71.4 (BioC devel). See here and here.

Both versions should become available to BioC 3.18 and BioC devel users via BiocManage::install() in the next 24 hours or so.

Note that I don't have an easy way to test this on Windows at the moment. Don't hesitate to let me know how that works for you. Thanks again.

Best,

H.

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Thanks, Hervé, for addressing this issue so quickly.

However, still only Biostrings 2.70.2 seems to be available.

Best,

Gerhard

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Should be available now: https://bioconductor.org/packages/3.18/Biostrings

(I forgot that we build/check release only every other day.)

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@gerhard-thallinger-1552
Last seen 4 months ago
Austria

Note that I don't have an easy way to test this on Windows at the moment. Don't hesitate to let me know how that works for you.

I upgraded to Biostrings 2.70.3; the file handles are now closed and file.remove() succeeds.

Thanks again,

Gerhard

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