error in Partitioning Genes into Expression Clusters

Question

[wes]

May I know how to solve the error below?

define_clusters_by_cutting_tree.pl -R fruit_DE_Unigenes.matrix.RData --Ptree 60
CMD: Rscript __tmp_define_clusters.R
Loading required package: BiocGenerics
Loading required package: parallel

Attaching package: ‘BiocGenerics’

The following objects are masked from ‘package:parallel’:

    clusterApply, clusterApplyLB, clusterCall, clusterEvalQ,
    clusterExport, clusterMap, parApply, parCapply, parLapply,
    parLapplyLB, parRapply, parSapply, parSapplyLB

The following objects are masked from ‘package:stats’:

    IQR, mad, sd, var, xtabs

The following objects are masked from ‘package:base’:

    anyDuplicated, append, as.data.frame, basename, cbind, colnames,
    dirname, do.call, duplicated, eval, evalq, Filter, Find, get, grep,
    grepl, intersect, is.unsorted, lapply, Map, mapply, match, mget,
    order, paste, pmax, pmax.int, pmin, pmin.int, Position, rank,
    rbind, Reduce, rownames, sapply, setdiff, sort, table, tapply,
    union, unique, unsplit, which, which.max, which.min

Welcome to Bioconductor

    Vignettes contain introductory material; view with
    'browseVignettes()'. To cite Bioconductor, see
    'citation("Biobase")', and for packages 'citation("pkgname")'.


Attaching package: ‘fastcluster’

The following object is masked from ‘package:stats’:

    hclust

Error in UseMethod("as.dendrogram") : 
  no applicable method for 'as.dendrogram' applied to an object of class "NULL"
Calls: heatmap.3 -> as.dendrogram
Execution halted
Error, cmd Rscript __tmp_define_clusters.R died with ret 256 at /home/cbr01/anaconda3/envs/wee_bfx/bin/define_clusters_by_cutting_tree.pl line 213

[lay_0]

I ran into the same exact error. Did you figure out?, thanks!

[Kevin Blighe]

The error is caused by R trying to use as.dendrogram() on a NULL object. Please explain more about the environment in which you are running this command. It looks like conda, granted, but which version of perl? Can you link to the program that you are using? What is the output of:

conda list