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broadinstitute / infercnv

Inferring CNV from Single-Cell RNA-Seq
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Error step 19 Error in type.convert.default(X[[i]], ...) : (converted from warning) 'as.is' should be specified by the caller; using TRUE > #506

Open Sa753 opened 1 year ago

Sa753 commented 1 year ago

Hi Christophe.

I got this error after installing version 1.15. It is even on the mock example in the package

This is my code

infercnv_obj2 = infercnv::run(infercnv_obj2, cutoff=0.1, # use 1 for smart-seq, 0.1 for 10x-genomics out_dir="human_infercnv2", # dir is auto-created for storing outputs cluster_by_groups=T, # cluster denoise=T, HMM = T, analysis_mode = 'sample' , num_ref_groups = 1, num_threads = 4) Step19

Error in type.convert.default(X[[i]], ...) : (converted from warning) 'as.is' should be specified by the caller; using TRUE

Thanks

GeorgescuC commented 1 year ago

Hi @Sa753 ,

What version of R are you using? And are all the other packages in R up to date? I remember a similar error occurring before one of the R version releases from some of the dependencies not being updated on the development branch yet for this change.

Regards, Christophe.

Sa753 commented 1 year ago

Hi Christophe,

I am using R 4.2.2.

GeorgescuC commented 1 year ago

Hi @Sa753 ,

I ran infercnv with the settings you posted on both the example object loadable with data() and the example dataset on github, but do not get the error in either case. Can you try to update all dependencies with update.packages() and then run infercnv again to see if the error persists? I would also recreate the infercnv object after the updates just in case.

Regards, Christophe.