Question: DESeq2 Error while loading from a conda Environment
0
gravatar for sangram_keshari
10 weeks ago by
sangram_keshari210 wrote:

I am trying to run DESeq2 from a conda environment. Installation was successful with all the dependencies as per conda, but while loading the library I came up with this error.

> library(DESeq2)
Loading required package: S4Vectors
Loading required package: stats4
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, colMeans,
    colnames, colSums, dirname, do.call, duplicated, eval, evalq,
    Filter, Find, get, grep, grepl, intersect, is.unsorted, lapply,
    lengths, Map, mapply, match, mget, order, paste, pmax, pmax.int,
    pmin, pmin.int, Position, rank, rbind, Reduce, rowMeans, rownames,
    rowSums, sapply, setdiff, sort, table, tapply, union, unique,
    unsplit, which, which.max, which.min


Attaching package: ‘S4Vectors’

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

    expand.grid

Loading required package: IRanges
Loading required package: GenomicRanges
Loading required package: GenomeInfoDb
Loading required package: SummarizedExperiment
Loading required package: Biobase
Welcome to Bioconductor

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

Loading required package: DelayedArray
Loading required package: matrixStats

Attaching package: ‘matrixStats’

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

    anyMissing, rowMedians


Attaching package: ‘DelayedArray’

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

    colMaxs, colMins, colRanges, rowMaxs, rowMins, rowRanges

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

        apply

Error: package or namespace load failed for ‘DESeq2’ in dyn.load(file, DLLpath = DLLpath, ...):
 unable to load shared object '/home/something/miniconda3/envs/something/lib/R/library/stringi/libs/stringi.so':
  libicui18n.so.54: cannot open shared object file: No such file or directory
In addition: Warning message:
multiple methods tables found for ‘pos’

I am not able to understand this error message. Help please.

conda deseq2 • 148 views
ADD COMMENTlink modified 10 weeks ago • written 10 weeks ago by sangram_keshari210
0
gravatar for sangram_keshari
10 weeks ago by
sangram_keshari210 wrote:

Tried to dig some more and I came up with this.

So there is some libicui18n.so.54 library conflict. So I installed this:

conda install -c conda-forge icu=54.1

Not exactly sure if this is the solution. But its working for now.

ADD COMMENTlink written 10 weeks ago by sangram_keshari210
Please log in to add an answer.

Help
Access

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.
Powered by Biostar version 2.3.0
Traffic: 973 users visited in the last hour