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benjjneb / decontam

Simple statistical identification and removal of contaminants in marker-gene and metagenomics sequencing data
https://benjjneb.github.io/decontam/
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Sample Data #8

Closed ghost closed 6 years ago

ghost commented 6 years ago

To whom it may concern,

I am just going through your sample data and I am running into a problem at the initial stages.

When trying to create the object 'ps' I am receiving a error as below

Error in gzfile(file, "rb") : cannot open the connection In addition: Warning message: In gzfile(file, "rb") : cannot open compressed file '', probable reason 'Invalid argument' All versions of relevant packages are up to date,

I am not sure of the origin of this problem. One suggestion was that the relevant sample files were not available.

Thanks for any help.

All the best, Maurice

benjjneb commented 6 years ago

Can you clarify what exact command you are running to cause that error? Is this from running the vignette?

benjjneb commented 6 years ago

Ah, found the bug. If you reinstall from github, the updated package version should work as expected, i.e. ps <- readRDS(system.file("extdata", "MUClite.rds", package="decontam")) will work.

Thanks for letting us know!