DESeq2 installs but then can't be brought in as a library
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@adisonkleinsasser-21720
Last seen 4.7 years ago

After installing DESeq2 on a computing cluster in a user's account, (using the command "conda install -c bioconda bioconductor-deseq2"), I tried to check on it to make sure it had installed properly, but received the following error (please see bottom):

> 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, 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

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

Loading required package: BiocParallel

Attaching package: ‘DelayedArray’

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

    colMaxs, colMins, colRanges, rowMaxs, rowMins, rowRanges

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

    aperm, apply, rowsum

Error: package or namespace load failed for ‘DESeq2’ in dyn.load(file, DLLpath = DLLpath, ...):
 unable to load shared object '/home/usd.local/bernie.wone/miniconda3/lib/R/library/stringi/libs/stringi.so':
  libicui18n.so.64: cannot open shared object file: No such file or directory

I am using R 3.6.1, and have also tried the method shown on this website: https://bioconductor.org/packages/release/bioc/html/DESeq2.html

please advise.

deseq2 R3.6.1 library(DESeq2) • 1.5k views
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Could you solve this error please? I am facing the same using R 4.2.1

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@martin-morgan-1513
Last seen 21 hours ago
United States

Generally, if you're trying to use bioconda then all packages should be installed using bioconda. I'd try to isolate the problem by verify / correcting the installation of stringi (via conda), which is being reported as the package that cannot be loaded.

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