Question

A problem occurs when running the monocle2

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yuheng_yang • 0

@6329b4d3

Last seen 9 weeks ago

Hangzhou,PRC

Fig 1 enter image description here

Fig 2 enter image description here

Fig 3 enter image description here

Fig 4 enter image description here

I encountered a problem when running monocle2. When I tried to open the file produced by the newCellDataSet function of the monocle package (see the Fig 1), an error occurred (see the Fig 2). I clicked on mycds in the Global Environment and found that almost all the contents of the mycds file were empty (see the Fig 3). I have tried many methods, including using upgrade_graph("mycds") (the result of this function is: Error in upgrade_graph(mycds): Not all inherits(graph, "igraph") are TRUE) (see the Fig 4). Switching to other versions of monocle did not solve the error either. My current R version is 4.5.1, the monocle package version is 2.36.0, and the igraph package version is 2.1.4. Has anyone encountered this problem before? How can I solve it?

monocle • 184 views

ADD COMMENT • link updated 2 hours ago by e.j.aaw.g.erm • 0 • written 9 weeks ago by yuheng_yang • 0

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ADD REPLY • link 2 hours ago e.j.aaw.g.erm • 0

score 0 · Answer 1 · 2025-11-07

Hi yuheng_yang,

This error arises from an incompatibility between Monocle 2.36.0 and the newer igraph 2.1.4, which causes the CellDataSet object to initialise incompletely and the graph to fail validation. Monocle 2 is no longer actively maintained and struggles with recent igraph releases.

To resolve it, downgrade igraph to a compatible version:

remotes::install_version("igraph", version = "2.0.3")

Restart your R session afterwards, then recreate the CellDataSet with newCellDataSet(). This should populate the object correctly and allow upgrade_graph() to run without issues.

If problems persist, I recommend migrating to Monocle 3, which is more robust with current R and package versions.

Kevin