Unable to load R package on Jupiter notebook

Asked 2 years ago, Updated 2 years ago, 116 views

I'm a beginner in programming.
I am trying to analyze using R on Jupiter notebook via miniconda.
It worked well until I added the kernel of R, but when I tried to load the R package, I got the following error:
What is the cause?

I use macOS 10.15.2 as my operating system.
We have deployed miniconda3-4.3.30 using pyenv1.2.15.

library(DESeq2)

Loading required package: S4 Vectors
Loading required package: stats4
Loading required package—BiocGenetics
Loading required package—parallel

Attaching package: 'BiocGenetics'

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, maply, match, mget,
    order, paste, pmax, pmax.int, pmin, pmin.int, Position, rank,
    rbind,Reduce,rounames,sapply,setdiff,sort,table,tapply,
    union, unique, unsplit, which, which.max, which.min


Attaching package: 'S4 Vectors'

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 introduction material; view with
    'browseVignettes()'.Tokite 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, rosum

Registered S3 methods overwritten by 'ggplot2':
  method from 
  [.quosures rlang]
  c.quosures rlang
  print.quosures rlang
Error: package or namespace load failed for 'DESeq2' indyn.load(file,DLLpath=DLLpath,...):
  Unable to load shared library '/Users/naga/.pyenv/versions/miniconda3-4.3.30/envs/py2_bio/lib/R/library/DESeq2/libs/DESeq2.dylib': 
  dlopen(/Users/naga/.pyenv/versions/miniconda3-4.3.30/envs/py2_bio/lib/R/library/DESeq2/libs/DESeq2.dylib,6)—Library not loaded: @rpath/libopenblasp-r0.3.7.dylib
  Referenced from: /Users/naga/.pyenv/versions/miniconda3-4.3.30/envs/py2_bio/lib/R/library/DESeq2/libs/DESeq2.dylib
  Reason—image not found 
Traceback:

1.library(DESeq2)
2.tryCatch({
 .     attr(package, "LibPath")<- which.lib.loc
 .     ns<-loadNamespace (package, lib.loc)
 .     env<-attachNamespace(ns, pos=pos, deps, exclude, include.
 . }, error=function(e){
 .     P<-if(!is.null(cc<-conditionCall(e))))) 
 .         paste("in", depth(cc)[1L])
 .     else"
 .     msg<-gettextf("package or namespace load failed for %s%s:\n%s", 
 .         sQuote(package), P, conditionMessage(e))
 .     if(logical.return) 
 .         message(paste("Error:", msg), domain=NA)
 .     else stop (msg, call.=FALSE, domain=NA)
 . })
3.tryCatchList(expr, classes, parentenv, handlers)
4.tryCatchOne(expr, names, parentenv, handlers[[1L]])
5. value [[3L]] (cond)
6.stop (msg, call.=FALSE, domain=NA)

r jupyter-notebook bioinformatics

2022-09-30 19:34

1 Answers

Judging from the error message, the shared library of OpenBLAS (libopenblasp-r0.3.7.dylib) cannot be found.This answer may be helpful.

This post was posted as a community wiki based on @metropolis' comments.


2022-09-30 19:34

If you have any answers or tips


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