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)
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.
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