Question

Issues installing GenomicAlignments

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Radhouane Aniba ▴ 240

@radhouane-aniba-4409

Last seen 8.6 years ago

Hello

I am having same issues installing GenomicAlignments and I am not sure whether it is a bug or it is a problem with the package ?

I get this error when I try to install it

http://pastebin.com/raw/KLthv7uM

Any ideas ?

Thanks

genomicalignments • 1.6k views

ADD COMMENT • link 8.6 years ago Radhouane Aniba ▴ 240

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Not sure what the problem is. Can you post your sessionInfo() ? Also, is it an option for you to upgrade to R-3.3.0 and Bioconductor 3.3? It may not solve this problem but it is recommended.

ADD REPLY • link 8.6 years ago Dan Tenenbaum ★ 8.2k

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Actually, it didnt want to install on a custom directory, but did install on the personal lib one, which is a bit strange to me

my sessioninfo

R version 3.2.3 (2015-12-10)
Platform: x86_64-pc-linux-gnu (64-bit)
Running under: Ubuntu 14.04.3 LTS

locale:
 [1] LC_CTYPE=en_US.UTF-8       LC_NUMERIC=C
 [3] LC_TIME=en_US.UTF-8        LC_COLLATE=en_US.UTF-8
 [5] LC_MONETARY=en_US.UTF-8    LC_MESSAGES=en_US.UTF-8
 [7] LC_PAPER=en_US.UTF-8       LC_NAME=C
 [9] LC_ADDRESS=C               LC_TELEPHONE=C
[11] LC_MEASUREMENT=en_US.UTF-8 LC_IDENTIFICATION=C

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

other attached packages:
[1] BiocInstaller_1.20.3

loaded via a namespace (and not attached):
[1] tools_3.2.3

ADD REPLY • link 8.6 years ago Radhouane Aniba ▴ 240

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You probably have some version mismatch between S4Vectors, IRanges, and GenomicAlignments. For us to tell we would need to see the output of your sessionInfo() after you've loaded the IRanges package with library(IRanges). Installing R 3.3 and BioC 3.3 from scratch as Dan suggested would solve these issues and is highly recommended anyway since the version of BioC you're using (BioC 3.2) is no more supported.

H.

ADD REPLY • link 8.6 years ago Hervé Pagès 16k

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Probably that means the existing package directory was created by an admin user and was not writable by the user you are running R as.

ADD REPLY • link 8.6 years ago Dan Tenenbaum ★ 8.2k