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dviraran / SingleR

SingleR: Single-cell RNA-seq cell types Recognition (legacy version)
GNU General Public License v3.0
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CreateSinglerObject Error #62

Open Kailewang opened 5 years ago

Kailewang commented 5 years ago

Hi, I installed singleR yesterday on the server, however, I got stuck after [1] "Fine-tuning round on top cell types (using 16 CPU cores):", several hours at "0%, ETA NA". However, the same code works fine on my local PC. Not sure why...

This morning I reinstall the package, after run the code, it also stuck after [1] "Fine-tuning round on top cell types (using 16 CPU cores):", but the error becomes: Error in textConnection("rval", "w", local = TRUE) : all connections are in use...

dviraran commented 5 years ago

Hi,

Haven't seen this error before, so not sure what can cause it. I think this error is from the parralel package, maybe there is an issue in registering 16 cores? try reducing the number of numCores to see if it has an effect.

Best, Dvir

Kailewang commented 5 years ago

Thanks for the reply, I just tested 1 core, still stuck there, did this package depend on something like python? This problem also appears on my another PC....

dviraran commented 5 years ago

The parallel computing only works on Unix-based OS (mac, linux, etc.). Which OS are you using?

Kailewang commented 5 years ago

I tested on our server (NAME="Red Hat Enterprise Linux Server", VERSION="7.6 (Maipo)"), it stuck, but other people in our lab tested on the same server, it works fine.... I also tried on mac os high seirra desktop (10.13), it stuck there too. But on my mac os laptop, it works fine.... Because I reinstall python on my own-folder in the server, not sure if that cause the problem.

dviraran commented 5 years ago

I really hope you figure this out and educate us. I am pretty sure that the problem is with the function pbmclapply from the pbmcapply package. That is the only non-trivial code in the fine-tuning step. Maybe try to reinstall that package.

Kailewang commented 5 years ago

Thanks! This problem was fixed after reinstall pbmcapply package. devtools::install_github("kvnkuang/pbmcapply", ref = "dev", force=T)