When I use identifySignatures from somaticsignatures package it throws me out this error. What do I need to change ?
identifySignatures(sca_mm,5,nmfDecomposition)
Error in (new("standardGeneric", .Data = function (x) :
unused arguments (model = list("NMFstd", 5, 0), method = "random")
I have encountered an exactly same problem. My code was working but I recently updated NMF packages (following biocLite suggestion). Then, when I ran the command, I had the error:
Thank you for the report. I have not been able to reproduce this issue with the same package versions as you have. Could you please post a complete example that I can rerun (from the starting of the R session until the error occurs) together with a complete output of the sessionInfo command?
Both NMF and SummarizedExperiment (through a package it Depends: on, DelayedArray) have implemented a seed generic. Usually a package can be confident that, when it references functions defined in it's own package, it gets only those functions. Here we have
Note the getGeneric() call that causes the problem -- it does not have a package= argument, and appears to use the search() path to find the generic. Since SummarizedExperiment was loaded after NMF, it finds the wrong generic.
I think this is a bug in the NMF implementation, and will try to contact the maintainer.
A work-around, which may not be satisfactory if you also want to use DelayedArray::seed(), is to use the new function conflictRules() defined in base R to exclude DelayedArray::seed() from being seen.
UPDATE This issue had already been reported to NMF, and is fixed in the devel version of the package. You can install the devel version of the package with
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Hi, Aslam
I have encountered an exactly same problem. My code was working but I recently updated NMF packages (following biocLite suggestion). Then, when I ran the command, I had the error:
sigs_nmf = identifySignatures(sca_mm, n_sigs, nmfDecomposition)
Error in (new("standardGeneric", .Data = function (x) :
unused arguments (model = list("NMFstd", 5, 0), method = "random")
> sessionInfo()
R version 3.5.0 (2018-04-23)
Platform: x86_64-w64-mingw32/x64 (64-bit)
Running under: Windows >= 8 x64 (build 9200)
Version of pacakges:
NMF_0.21.0
SomaticSignatures_2.16.0
VariantAnnotation_1.26.1
Thank you for the report. I have not been able to reproduce this issue with the same package versions as you have. Could you please post a complete example that I can rerun (from the starting of the R session until the error occurs) together with a complete output of the sessionInfo command?