Error in nn.d^2 : non-numeric argument to binary operator

[MMriran]

Dear sir, it is a great work that you designed singleR, moreover,I just upgraded to SingleR from bioconductor. And，after I ran SingleR with your "Using the built-in references" part code,there was an error"Error in nn.d^2 : non-numeric argument to binary operator"

library(SingleR) hpca.se <- HumanPrimaryCellAtlasData() hpca.se library(scRNAseq) hESCs <- LaMannoBrainData('human-es') hESCs <- hESCs[,1:100] library(scater) common <- intersect(rownames(hESCs), rownames(hpca.se)) hpca.se <- hpca.se[common,] hESCs <- hESCs[common,] hESCs <- logNormCounts(hESCs) pred.hpca <- SingleR(test = hESCs, ref = hpca.se, labels = hpca.se$label.main)

so how can i solve this problem？ Best wishes!

Yours sincerely, CHEN

[MediciPrime]

I have the same problem, just updated yesterday and today SingleR is running into that error. I am literally running the code from part 2 of the vignette and having the same problem. Please fix this @dviraran , the bioconductor version was working great before the update.

[MediciPrime]

Hi @MMriran I figured out the problem. You need to downgrade your version of BiocNeighbors from 1.3.5 to 1.3.3. Some updates were pushed onto it last weekend that have bugs in them.

Use code below to downgrade your BiocNeighbors Package: devtools::install_github("LTLA/BiocNeighbors", ref="be43721")

Once its installed restart your R session and assuming you installed SingleR using Bioconductor, it should all work fine from there.

[MMriran]

hi@MediciPrime,thank you!!!! however,after I ran the codedevtools::install_github("LTLA/BiocNeighbors", ref="be43721") there was another error “_### ERROR: failed to lock directory 'C:/Program Files/R/R-3.6.1/library' for modifying Try removing 'C:/Program Files/R/R-3.6.1/library/00LOCK-BiocNeighbors' Error: Failed to install 'BiocNeighbors' from GitHub: (converted from warning) installation of package ‘C:/Users/Administrator/AppData/Local/Temp/RtmpGiADOX/file44b02c823554/BiocNeighbors1.3.3.tar.gz’ had non-zero exit status ”.

[dviraran]

Hi,

Yes, this is a problem because of a change in BiocNeighbors, and will be fixed with the next build of bioC devel. We are working on fixing this.

In the future, to get faster response, strongly suggest raising issues in https://github.com/LTLA/SingleR

Best, Dvir

[MMriran]

Yes！thant you for your reply！ @dviraran

[MediciPrime]

@MMriran the alternative approach to downgrading BiocNeighbors would be to upgrade SingleR. Since BiocNeighbors 1.3.5 is made to run on the newest version of SingleR which hasn't been uploaded to Bioconductor.

I would run the following command: devtools::install_github("LTLA/SingleR", ref="0c10e16")

For your error above I would try doing what the error suggests, "Try removing C:/Program Files/R/R-3.6.1/library/00LOCK-BiocNeighbors" although I am not positive on how to solve it.

Goodluck!