issue with loading methylKit package

[Aktan Alpsoy]

Hi,

I have been using methylKit since last week. I have had no issue with package loading and executing methyKit functions so far. Yesterday, when I tried to load the package via library("methylKit") for a different session, it prompted an error in the console as : 

> library("methylKit")
Error: package or namespace load failed for ‘methylKit’:
 object ‘key<-’ is not exported by 'namespace:data.table'

I tried reinstalling methylKit, data.table, R, Rstudio but none of them helped. I tried installing methylKit into a machine that never had it installed; when I called the package it prompted the same error. Please find the minimal input and output for the error and my sessionInfo in the attached text file.

Kind regards,

Aktan

[Aktan Alpsoy]

Hi again,

It seems that update to data.table version 1.17 is the problem. When I keep it 1.16.4 it loads OK. 

Kind regards,

[Alexander Blume]

Hi Aktan,

Thanks for reporting this! I have  seen a similar issue in the Bioconductor build system, but haven’t found time to fix this.
Currently your proposed fix is the best way to solve the issue.

Best,
Alex

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[Josephine]

How do you make sure it loads using 1.16.4. I am running into issues

[Aktan Alpsoy]

With 1.17 loaded, I cannot load methylKit (library("methylKit") prompts errror). No error with data.table 1.16.4 (or even earlier versions, I guess).

Some other packages may also be using data.table as an auxiliary package and when prompted, update to data.table needs to be avoided. I'd check packageVersion("data.table") from time to time.

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[Alexander Blume]

I pushed a fix to the github repository (commit 5c30347630bc064d7aefc918923f723671f35253).
The bioc repository will follow soon.

Best,
Alex

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