Error: could not find function "try_fetch" about clustree

[MANZHAOHUI]

I am dealing with single cell seurat object, using umap as reduction method with the codes as below:
combined.integrated <- RunUMAP(combined.integrated, dims = 1:30)
combined.integrated <- FindNeighbors(combined.integrated, reduction = "umap", dims = 1:2)
combined.int.clustree <- FindClusters(
object = combined.integrated,
method = "igraph",
resolution = c(0.1, 0.2, 0.3, 0.4, 0.5, 0.6)
)
[email protected] [1:3, ]
orig.ident nCount_RNA nFeature_RNA Sex age sampID
01_38_AAACCCACAGTGTACT-1 PD 1696 1010 Female 80 01_38
01_38_AAACCCAGTTGGGATG-1 PD 12040 3389 Female 80 01_38
01_38_AAACCCATCCAGCACG-1 PD 2839 1540 Female 80 01_38
percent.mt PMI nCount_SCT nFeature_SCT predicted.id
01_38_AAACCCACAGTGTACT-1 4.126625 7.5 3471 1047 Oligo
01_38_AAACCCAGTTGGGATG-1 1.978344 7.5 4514 2214 Oligo
01_38_AAACCCATCCAGCACG-1 6.519592 7.5 3513 1539 Oligo
prediction.score.Inh prediction.score.Exc
01_38_AAACCCACAGTGTACT-1 0 0
01_38_AAACCCAGTTGGGATG-1 0 0
01_38_AAACCCATCCAGCACG-1 0 0
prediction.score.Oligo prediction.score.Astro
01_38_AAACCCACAGTGTACT-1 1 0
01_38_AAACCCAGTTGGGATG-1 1 0
01_38_AAACCCATCCAGCACG-1 1 0
prediction.score.Micro prediction.score.OPC
01_38_AAACCCACAGTGTACT-1 0 0
01_38_AAACCCAGTTGGGATG-1 0 0
01_38_AAACCCATCCAGCACG-1 0 0
prediction.score.Endo prediction.score.VLMC
01_38_AAACCCACAGTGTACT-1 0 0
01_38_AAACCCAGTTGGGATG-1 0 0
01_38_AAACCCATCCAGCACG-1 0 0
prediction.score.max adjusted.prediction.score.max
01_38_AAACCCACAGTGTACT-1 1 1
01_38_AAACCCAGTTGGGATG-1 1 1
01_38_AAACCCATCCAGCACG-1 1 1
integrated_snn_res.0.1 integrated_snn_res.0.2
01_38_AAACCCACAGTGTACT-1 0 10
01_38_AAACCCAGTTGGGATG-1 3 15
01_38_AAACCCATCCAGCACG-1 2 9
integrated_snn_res.0.3 integrated_snn_res.0.4
01_38_AAACCCACAGTGTACT-1 1 36
01_38_AAACCCAGTTGGGATG-1 5 39
01_38_AAACCCATCCAGCACG-1 11 13
integrated_snn_res.0.5 integrated_snn_res.0.6
01_38_AAACCCACAGTGTACT-1 13 6
01_38_AAACCCAGTTGGGATG-1 2 36
01_38_AAACCCATCCAGCACG-1 9 9
seurat_clusters
01_38_AAACCCACAGTGTACT-1 6
01_38_AAACCCAGTTGGGATG-1 36
01_38_AAACCCATCCAGCACG-1 9

cluster_tree <- clustree(combined.int.clustree,prefix = "integrated_snn_res.")

all the steps worked except for the last one 'clustree(combined.int.clustree,prefix = "integrated_snn_res.")'
the error is
"Error in try_fetch(utils::getFromNamespace(algorithm, "igraph"), error = function(cnd) { :
could not find function "try_fetch" "

thank you.

[lazappi]

Hi @MANZHAOHUI

This looks like a problem with your installation of the {igraph} package. I found try re-installing that and seeing if that helps. If not you may have to ask the package developers, I don't think this is an issue with {clustree}.

[MANZHAOHUI]

thank you.