Issue with GenomicRanges in windows 3.3.1
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@lavinia-gordon-6486
Last seen 7.6 years ago

Hi

When trying to install GenomicRanges I encounter the following error (see below). I have started with a completely fresh install.  Installed using biocLite.

with regards

Lavinia Gordon.

Loading required package: IRanges
Loading required package: GenomeInfoDb
Error : Function found when exporting methods from the namespace ‘XVector’ which is not S4 generic: ‘compare’
Error: package or namespace load failed for ‘GenomicRanges’
> sessionInfo()
R version 3.3.1 (2016-06-21)
Platform: x86_64-w64-mingw32/x64 (64-bit)
Running under: Windows 7 x64 (build 7601) Service Pack 1

locale:
[1] LC_COLLATE=English_Australia.1252  LC_CTYPE=English_Australia.1252    LC_MONETARY=English_Australia.1252 LC_NUMERIC=C                       LC_TIME=English_Australia.1252    

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

other attached packages:
[1] GenomeInfoDb_1.6.3  IRanges_2.6.1       S4Vectors_0.10.2    BiocGenerics_0.18.0

loaded via a namespace (and not attached):
[1] zlibbioc_1.16.0 tools_3.3.1    

 

 

genomicranges windows 7 • 1.7k views
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For a second I thought the title said "Issue with GenomicRanges in Windows 3.1"... Has anyone tested R/Bioc support for that? :)

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@martin-morgan-1513
Last seen 6 weeks ago
United States

Somehow, GenomeInfoDb is version 1.6.3 (Bioconductor 3.2, previous) whereas IRanges is 2.6.1 (Bioc 3.3, current). biocLite() should have asked if you'd like to update old packages. Check the output of BiocInstaller::biocValid() and update as appropriate.

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That is an awesome response time Martin!, thank you.

Biocinstaller::biocValid does highlight a number of issues, I'll address them now.  This is interesting as I am working off a completely fresh install.

Thank you so much for this, it is appreciated.

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.libPaths() indicates the paths where R looks for libraries. Likely .libPaths() includes a path shared between the previous and new installation.

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