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Question: Error in export ifelse from IRanges
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gravatar for dalibor.miklik
8 months ago by
dalibor.miklik0 wrote:

Hello,

I am using the package restrSiteUtils version 1.2.8. Until now, everything was fine but now when I want to start working with the package, following error arise:

> library(restrSiteUtils)
Error: package or namespace load failed for ‘restrSiteUtils’:
 object ‘ifelse’ is not exported by 'namespace:IRanges'

I have just recently updated R and all Bioconductor packages that I use. Is IRanges package changed somehow so exporting ifelse doesn't work? And does anybody have an idea how could I overcome this error so I could use my desired package?

Thanks in advance for any advice

Dalibor

> sessionInfo()
R version 3.4.3 (2017-11-30)
Platform: x86_64-w64-mingw32/x64 (64-bit)
Running under: Windows 8.1 x64 (build 9600)

Matrix products: default

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

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

other attached packages:
[1] GenomicRanges_1.30.0 GenomeInfoDb_1.14.0  IRanges_2.12.0       S4Vectors_0.16.0     BiocGenerics_0.24.0

loaded via a namespace (and not attached):
[1] zlibbioc_1.24.0        compiler_3.4.3         XVector_0.18.0         GenomeInfoDbData_1.0.0 RCurl_1.95-4.10        Biostrings_2.46.0     
[7] bitops_1.0-6
ADD COMMENTlink modified 8 months ago by James W. MacDonald47k • written 8 months ago by dalibor.miklik0
0
gravatar for James W. MacDonald
8 months ago by
United States
James W. MacDonald47k wrote:

This is a question you should be asking of the maintainer for restrSiteUtils, which isn't a Bioconductor package. This site is intended to support Bioconductor packages, not other packages that may make use of some Bioconductor packages.

You might point out that IRanges no longer defines nor exports ifelse, but instead ifelse2:

commit 2efbf8d4bd5f4b94174226c79b2b0293f7b11a1b
Author: Michael Lawrence <lawremi@iastate.edu>
Date:   Fri Jul 7 05:28:37 2017 +0000

    replace ifelse generic and methods with ifelse2 (eager semantics)
    
    
    git-svn-id: file:///home/git/hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/IRanges@131030 bc3139a8-67e5-0310-9ffc-ced21a209358

 

ADD COMMENTlink written 8 months ago by James W. MacDonald47k
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