Can you reproduce this error using the tutorial dataset?

When i use tutorial dataset,this error does not occur.
Is there something wrong with my data? (but my data comes from 10X cellranger-atac,I didn't do anything else to fragments.tsv.gz file.)
How can I deal with this error?

Run into the same error here. Hope to see update on the issue.

We will need more information in order to help since we cannot reproduce this error. If you can create a minimal example, including input files, that would be helpful.

The R^2 values of my samples all < 0.9, that mean I can skip this step(filterDoublets)?

No, that is not the correct interpretation. see #173 (comment) for an explanation

Thanks. I've read the question( #173 (comment)).
And how can I create a minimal example so that you can better solve this problem?

Ideally, take a random 50,000 lines (or the first 50,000 if you prefer) of your fragment file and see if you get the same error. If so, provide us with the small fragment file and the code you used that resulted in the error.

hi!
When i run filterDoublets(ArchRProj = proj1),I got an error "Error in as.POSIXct.numeric(e) : 'origin' must be supplied".
And i don't konw how to solve the problem.There is nothing wrong with the previous steps.
I want to know how to deal with this problem, continue to analyze the data (My data comes from 10x)
Thanks!

When does this happen? Towards the end or beginning? Is there a logfile you can share?

@jgranja24 ,This step does not generate any logfiles.
it show me this:

@rcorces ,I'm sorry for what I said earlier(I guess I forgot to run the tutorial dataset)
Today,I run tutorial dataset, the same error occurred……emmmm,do you have any suggestions?
Thanks!

@Meggie-MH are you also running on Windows? We arent currently supporting windows and I should make that more clear on the home page.

@jgranja24 - I think this is a problem related to date format conversion on Windows from Sys.time(). https://rdrr.io/r/base/Sys.time.html

@rcorces No, I was running on Mac. I also tried the tutorial dataset and ran into the same error from filterDoublets. The only thing I did different from the tutorial was creating arrow files by inputting individual fragments.tsv.gz and then combined all the arrow files into one character vector before running the following the steps. For some reasons, it takes infinite time to createarrowfiles directly from 'hemefragments' folder which contains three tsv.gz datasets. Not sure if that's the step starts with this issue.

@rcorces Woohoo, rewrite the function works! Thanks a lot :)

• Back to your previous question, it does't avoid the error when running > summary <- c("Date" = as.Date(Sys.time(), origin = "1970-01-01"), test1 = 1, test2 = "two")

First of all, thanks for creating such an amazing tool! I have been such a huge fan.

Unfortunately I'm running into the same problem. The same error happens when filtering doublets. (I m running it on Linux)

proj <- filterDoublets(ArchRProj = proj,cutEnrich=5)

Error info

Error in as.POSIXct.numeric(e): 'origin' must be supplied
Traceback:
1. filterDoublets(ArchRProj = proj, cutEnrich = 5)
2. addProjectSummary(ArchRProj = ArchRProj, name = "filterDoublets", 
 .     summary = c(Date = Sys.time(), cutEnrich = cutEnrich, cutScore = cutScore, 
 .         filterRatio = filterRatio))
3. append(pS, SimpleList(summary))
4. SimpleList(summary)
5. c(Date = Sys.time(), cutEnrich = cutEnrich, cutScore = cutScore, 
 .     filterRatio = filterRatio)
6. c.POSIXct(Date = Sys.time(), cutEnrich = cutEnrich, cutScore = cutScore, 
 .     filterRatio = filterRatio)
7. .POSIXct(c(unlist(lapply(list(...), function(e) unclass(as.POSIXct(e))))))
8. unlist(lapply(list(...), function(e) unclass(as.POSIXct(e))))
9. lapply(list(...), function(e) unclass(as.POSIXct(e)))
10. FUN(X[[i]], ...)
11. as.POSIXct(e)
12. as.POSIXct.numeric(e)
13. stop("'origin' must be supplied")

Rewriting the function as suggested by @jgranja24 works for me too.

@Meggie-MH - thanks for checking. We will update the dev branch with the fix from @jgranja24

@huidongchen - can you confirm which version of R you are using? Presumably >4.0?

@huidongchen - can you confirm which version of R you are using? Presumably >4.0?

Thanks for your quick reply! Yes, I'm using R 4.0.1

@jgranja24 ,Thanks for your help!
@rcorces ,And I've run this function successfully,Using the function @jgranja24 wrote.
Thanks again for all your help! (I also use R 4.0.1)

I can confirm this problem. The fixed function worked for me and I am happy to have found the information in this thread!

My system:

R version 4.0.2 (2020-06-22) -- "Taking Off Again"
Copyright (C) 2020 The R Foundation for Statistical Computing
Platform: x86_64-apple-darwin19.5.0 (64-bit)

@jgranja24 can you make the relevant update(s) in dev? This gets rid of the project summary so if anything downstream uses the summary that will also need to change

Facing the Same Issue on R 4.0.1! Running filterdoublet functions works well

Hi @Meggie-MH can you try running this filterDoublets function where we just remove the line causing the issue

filterDoublets <- function(ArchRProj = NULL, cutEnrich = 1, cutScore = -Inf, filterRatio = 1){

  fn <- unclass(lsf.str(envir = asNamespace("ArchR"), all = TRUE))
    for (i in seq_along(fn)) {
        tryCatch({
            eval(parse(text = paste0(fn[i], "<-ArchR:::", fn[i])))
        }, error = function(x) {
        })
    }

  .validInput(input = ArchRProj, name = "ArchRProj", valid = c("ArchRProj"))
  .validInput(input = cutEnrich, name = "cutEnrich", valid = c("numeric"))
  .validInput(input = cutScore, name = "cutScore", valid = c("numeric"))
  .validInput(input = filterRatio, name = "filterRatio", valid = c("numeric"))

  if(any(grepl("filterDoublets", names(ArchRProj@projectSummary)))){
    stop("Already ran filterDoublets on ArchRProject! Cannot be re-ran on an ArchRProject!")
  }

  df <- getCellColData(ArchRProj, c("Sample", "DoubletEnrichment", "DoubletScore"))
  splitDF <- split(seq_len(nrow(df)), as.character(df$Sample))

  cellsFilter <- lapply(splitDF, function(y){

    x <- df[y, ,drop = FALSE]

    n <- nrow(x)

    x <- x[order(x$DoubletEnrichment, decreasing = TRUE), ]
    
    if(!is.null(cutEnrich)){
      x <- x[which(x$DoubletEnrichment >= cutEnrich), ]
    } 
    
    if(!is.null(cutScore)){
      x <- x[which(x$DoubletScore >= cutScore), ]
    } 

    if(nrow(x) > 0){
      head(rownames(x), filterRatio * n * (n / 100000))
    }else{
      NULL
    }

  }) %>% unlist(use.names=FALSE)

  message("Filtering ", length(cellsFilter), " cells from ArchRProject!")
  tabRemove <- table(df[cellsFilter,]$Sample)
  tabAll <- table(df$Sample)
  samples <- unique(df$Sample)
  for(i in seq_along(samples)){
    if(!is.na(tabRemove[samples[i]])){
      message("\t", samples[i], " : ", tabRemove[samples[i]], " of ", tabAll[samples[i]], " (", round(100 * tabRemove[samples[i]] / tabAll[samples[i]], 1),"%)")
    }else{
      message("\t", samples[i], " : ", 0, " of ", tabAll[samples[i]], " (0%)")
    }
  }

  if(length(cellsFilter) > 0){
    
    ArchRProj@cellColData <- ArchRProj@cellColData[rownames(ArchRProj@cellColData) %ni% cellsFilter,,drop=FALSE]

  }
  
  ArchRProj

}

@jgranja24 - can you make this update on dev?

This is now fixed on the release branch

devtools::install_github("GreenleafLab/ArchR", ref="release_1.0.0", repos = BiocManager::repositories())

Closing this issue, if you have any more troubles please open a new issue!

Best

Jeff