IRanges reduce Function Crashes R session
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e0saka02 • 0
@e0saka02-7777
Last seen 8.9 years ago
United States

I am using R x64 3.2.0 with Bioconductor version 3.1  and IRanges version 2.2.1.

When I try to run reduce function, R section stops working with fatal error. One time I saw an error related to realloc.

In order to make sure that memory is not issue, I tried a simple IRanges example given in the overview document.

ir <- IRanges(c(1, 8, 14, 15, 19, 34, 40), width = c(12, 6, 6, 15, 6, 2, 7))

reduce(ir)

I tried same example with older versions and did not have any problem.

Is there something I am missing with the new version of Bioconductor and IRanges?

 

IRanges • 838 views
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You need to always include the sessionInfo().

> ir <- IRanges(c(1, 8, 14, 15, 19, 34, 40), width = c(12, 6, 6, 15, 6, 2, 7))
> reduce(ir)
IRanges of length 3
    start end width
[1]     1  29    29
[2]    34  35     2
[3]    40  46     7
> sessionInfo()
R version 3.2.0 (2015-04-16)
Platform: i386-w64-mingw32/i386 (32-bit)
Running under: Windows 7 x64 (build 7601) Service Pack 1

locale:
[1] LC_COLLATE=English_United States.1252
[2] LC_CTYPE=English_United States.1252   
[3] LC_MONETARY=English_United States.1252
[4] LC_NUMERIC=C                          
[5] LC_TIME=English_United States.1252    

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

other attached packages:
[1] IRanges_2.2.1       S4Vectors_0.6.0     BiocGenerics_0.14.0

 

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Entering edit mode
@herve-pages-1542
Last seen 1 day ago
Seattle, WA, United States

Hi,

On April 28, I introduced a bug in the devel version of S4Vectors (0.7.1) that I fixed 2 days later in S4Vectors 0.7.2. The bug was causing exactly that kind of crash so I suspect you're using BioC devel and you still have S4Vectors 0.7.1 (please always show your sessionInfo() when you report a bug, it is essential information for troubleshooting). Please update your packages with biocLite() (call it with no arguments). It's actually recommended to do this on a regular basis e.g. once or twice a week in order to keep your installation up-to-date.

Cheers,

H.

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