GreenleafLab / ArchR

ArchR : Analysis of Regulatory Chromatin in R (www.ArchRProject.com)
MIT License
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Error report: getMarkerFeatures(): "Error Found Iteration 1 : [1] "Error in .logError(e, ..." #1931

Closed OOAAHH closed 1 year ago

OOAAHH commented 1 year ago

I meet this error as well as i analysising my frangment files. It happened again that when i follow the mannual in your official site ( I use the same data as mannual )

inputFiles <- getTutorialData("Hematopoiesis")
inputFiles

And here is my code that it meet the same error:

markersGS <- getMarkerFeatures(
    ArchRProj = projHeme2, 
    useMatrix = "GeneScoreMatrix", 
    groupBy = "Clusters",
    bias = c("TSSEnrichment", "log10(nFrags)"),
    testMethod = "wilcoxon"
)

This is the traceback: ArchR-getMarkerFeatures-3cd1a0e8be9-Date-2023-04-20_Time-01-47-33.log

Error Found Iteration 1 : 
[1] "Error in .logError(e, fn = \".sparseMatWilcoxon\", info = seqnames[y], errorList = errorList, : \n Exiting See Error Above\n"
<simpleError in .logError(e, fn = ".sparseMatWilcoxon", info = seqnames[y], errorList = errorList, logFile = logFile): Exiting See Error Above>
Error Found Iteration 2 : 
[1] "Error in .logError(e, fn = \".sparseMatWilcoxon\", info = seqnames[y], errorList = errorList, : \n Exiting See Error Above\n"
<simpleError in .logError(e, fn = ".sparseMatWilcoxon", info = seqnames[y], errorList = errorList, logFile = logFile): Exiting See Error Above>
Error Found Iteration 3 : 
[1] "Error in .logError(e, fn = \".sparseMatWilcoxon\", info = seqnames[y], errorList = errorList, : \n Exiting See Error Above\n"
[ArchR-getMarkerFeatures-3cd1a0e8be9-Date-2023-04-20_Time-01-47-33.log](https://github.com/GreenleafLab/ArchR/files/11285439/ArchR-getMarkerFeatures-3cd1a0e8be9-Date-2023-04-20_Time-01-47-33.log)

<simpleError in .logError(e, fn = ".sparseMatWilcoxon", info = seqnames[y], errorList = errorList, logFile = logFile): Exiting See Error Above>
Error Found Iteration 4 : 
[1] "Error in .logError(e, fn =
rcorces commented 1 year ago

Hi @OOAAHH! Thanks for using ArchR! I am currently on vacation and will not be responding to any issues or discussion threads until 5/5.
Please make sure that your post belongs in the Issues section. Only bugs and error reports belong in the Issues section. Usage questions and feature requests should be posted in the Discussions section, not in Issues.
It is worth noting that there are very few actual bugs in ArchR. If you are getting an error, it is probably something specific to your dataset, usage, or computational environment, all of which are extremely challenging to troubleshoot. As such, we require reproducible examples (preferably using the tutorial dataset) from users who want assistance. If you cannot reproduce your error, how will we be able to help? Before going through the work of making a reproducible example, search the previous Issues, Discussions, function definitions, or the ArchR manual and you will likely find the answers you are looking for. If your post does not contain a reproducible example, it is unlikely to receive a response.
1. If you've encountered an error, have you already searched previous Issues to make sure that this hasn't already been solved? 2. Can you recapitulate your error using the tutorial code and dataset? If so, provide a reproducible example. 3. Did you post your log file? If not, add it now. 4. Remove any screenshots that contain text and instead copy and paste the text using markdown's codeblock syntax (three consecutive backticks). You can do this by editing your original post.

OOAAHH commented 1 year ago

Errors can be repeated. But once I built the computing environment from scratch, it worked fine both the tutorial data and mine. It‘s really weird and I can't really locate the cause of the error, either on my mac or linux server.

错误可以复现。 我重置了我整个计算环境后问题解决了。而最初我使用教程数据和我自己的数据时,这个问题不断复现。 无论是在我的mac上还是服务器上,我都没办法定位问题出在哪里。