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Error in 'cds <- orderCells(cds)' #521

Open liyiwang0725 opened 3 weeks ago

liyiwang0725 commented 3 weeks ago

Hi everyone, I am using monocle2 to perform psedotime analysis. I met an error when it running: cds <- reduceDimension(cds, max_components = 2, method = 'DDRTree') cds <- orderCells(cds)

Error:
! `nei()` was deprecated in igraph 2.1.0 and is now defunct.
ℹ Please use `.nei()` instead.
Run `rlang::last_trace()` to see where the error occurred.
Warning message:
The `neimode` argument of `dfs()` is deprecated as of igraph 1.3.0.
ℹ Please use the `mode` argument instead.
ℹ The deprecated feature was likely used in the igraph package.
  Please report the issue at <https://github.com/igraph/rigraph/issues>.
This warning is displayed once every 8 hours.
Call `lifecycle::last_lifecycle_warnings()` to see where this warning was generated.

How to figure it out? My version: R 4.4.1 monocle 2.33.0 igraph 2.1.1 Thanks for your help!

qes2 commented 3 weeks ago

I have the same problem.

2ZHOU4 commented 3 weeks ago

I have the same problem.

juanjuanmei commented 1 week ago

I have the same problem..who can help me.thank you very much!!!!!

qes2 commented 1 week ago

I have the same problem..who can help me.thank you very much!!!!!

To solve this problem, simply downgrade the igraph. Go to the following link and install version 2.0.3 to restart the R session.

https://cran.rstudio.com/bin/macosx/big-sur-arm64/contrib/4.2/igraph_2.0.3.tgz

juanjuanmei commented 1 week ago

I have the same problem..who can help me.thank you very much!!!!!

To solve this problem, simply downgrade the igraph. Go to the following link and install version 2.0.3 to restart the R session.

https://cran.rstudio.com/bin/macosx/big-sur-arm64/contrib/4.2/igraph_2.0.3.tgz

thank you reply my question so quickly，this problem is solved!

tcliu2000 commented 2 days ago

however, many packages depend on igraph function. if changed the version, how to solve another issues? anyway when installing it,,,, install.packages("./igraph_2.0.3.tgz", repos = NULL, type="source") WARNING: Rtools is required to build R packages but is not currently installed. Please download and install the appropriate version of Rtools before proceeding:

https://cran.rstudio.com/bin/windows/Rtools/

jinyun529 commented 1 day ago

I encountered the same issue where I couldn't load igraph after downloading version 2.0.3 due to too many dependencies. Could you please help me resolve this problem? Your assistance would be greatly appreciated. Thank you.