Bio3d installation in Ubuntu 20.04

[Former user]

Hi, I was using bio3d in R version 3.6.3 installed in my ubuntu v20.04 system, but was not able to use functions like lmi, betweeness. Can you please help me regarding this.

[Xinqiu Yao]

Hi,

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Can you provide more details, including the commands you used and error messages you got?

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[gauri Thapa]

cij2 <- lmi(trj2[, inds$xyz])
Error in lmi(trj2[, inds$xyz]) : could not find function "lmi"

node.betweenness <- betweenness(net$network)
Error in betweenness(net$network) : could not find function "betweenness"

While command like read.pdb, fit.xyz are working fine.

I earlier used R v 3.4.4 and all the above commands worked fine in that version. I am unable to install this same version in my Ubuntu 20.04v.

Thank you so much for your help.

Gauri

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[Xinqiu Yao]

The lmi() function is obsolete. Use dccm(trj2[, inds$xyz], method="lmi") instead.

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betweenness() is a function from the igraph package. Use either igraph::betweenness() or library(igraph) at the beginning.

[gauri Thapa]

Thank you very much.