[Bioc-devel] Error for voom() in limma package

[Gordon K Smyth]

Dear Lan,

When reporting a possible bug in an R package, the minimum information that is usually reported is the version numbers of R and the package (using sessionInfo) and the code leading up to the error. You haven't provided any of that information, so I hope you don't mind if I take a wild guess at what is happening.

If you look at the package description for the current release of limma, you will see that it depends on R 3.6.0 or higher. If you use the recommended installation procedures for Bioconductor packages, you will always get the right version of limma for the right version of R.

I am guessing that, instead of using the Bioconductor installation procedures, you have instead copied code from the current version of limma and have tried to run it in an older version of R (R 3.5.X or earlier).

I recommend that you install the current version of R and install limma by

    library(BiocManager)
    install("limma")

Then everything will work correctly.

Best wishes
Gordon

------------------------------------------
Professor Gordon K Smyth
Joint Head, Bioinformatics Division
Walter and Eliza Hall Institute of Medical Research

From: Lan Huong Nguyen <lanhuong using stanford.edu>
Sent: Wednesday, 19 June 2019 1:57 AM
To: bioc-devel using r-project.org; Gordon K Smyth <smyth using wehi.edu.au>
Subject: Error for voom() in limma package

Hi,

I am having an issue with running voom function. I believe it is caused be the line 73 in the voom.R file.

f <- approxfun(l, rule = 2, ties = list("ordered", mean))

The third argument causes the following error:

 Error in get(as.character(FUN), mode = "function", envir = envir) :
  object 'ties' of mode 'function' was not found

Please let me know how the issue can be addressed.

Best,
Lan
--
Lan Huong Nguyen
PhD Candidate
ICME Stanford University
Huang Building 475 Via Ortega,
Stanford, CA 94305
(650) 723-2560<https://www.google.com/search?q=icme&oq=icme&aqs=chrome..69i57j69i60j69i65l3j69i60.1858j0j7&sourceid=chrome&ie=UTF-8>

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