Question: DESeq2 installs but then can't be brought in as a library
0
gravatar for adison.kleinsasser
21 days ago by
adison.kleinsasser0 wrote:

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.

ADD COMMENTlink modified 21 days ago by Martin Morgan ♦♦ 23k • written 21 days ago by adison.kleinsasser0
Answer: DESeq2 installs but then can't be brought in as a library
0
gravatar for Martin Morgan
21 days ago by
Martin Morgan ♦♦ 23k
United States
Martin Morgan ♦♦ 23k wrote:

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.

ADD COMMENTlink written 21 days ago by Martin Morgan ♦♦ 23k
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