Error in 'cds <- orderCells(cds)'

[liyiwang0725]

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!

[2ZHOU4]

I have the same problem.

[juanjuanmei]

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

[qes2]

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]

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]

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/

• installing binary package 'igraph' ...
  Warning in system(paste("mv -f", shQuote(instdir), shQuote(file.path(lockdir, :
  'mv' not found
  Warning in system(paste("cp -R .", shQuote(instdir), "|| (", TAR, "cd - .| (cd", :
  'cp' not found
  ERROR: installing binary package failed
• removing 'E:/Program Files/R/R-4.4.1/library/igraph'
  Warning in install.packages :
  The exit status value was not 0 when installing the package './igraph_2.0.3.tgz'.

[jinyun529]

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.

[1547175390]

I encountered the problem that “package ‘./igraph_2.0.3.tgz’ is not available for this version of R”

[Ktek28]

did anyone solve this problem? I am facing the same issue. I downgraded my igraph version but then many other functions like ggtitle, dimplot arent working!

[KirakiraZLY]

I am encountering the same issue. 😅😅😅