Problem with DESeq2
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Norbert ▴ 10
@a5fb06e6
Last seen 10 weeks ago
Hungary

I have got an Apple MacBook Air M1 with R version 4.2.2. I installed DESeq2 but I can not run it. How could I resolve this error?

I tried run DESeq2 with this code:

library("DESeq2")

I got this error:

```Loading required package: S4Vectors Loading required package: stats4 Loading required package: BiocGenerics

Attaching package: ‘BiocGenerics’

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

    IQR, mad, sd, var, xtabs

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

    Filter, Find, Map, Position, Reduce, anyDuplicated, append,
    as.data.frame, basename, cbind, colnames, dirname, do.call,
    duplicated, eval, evalq, get, grep, grepl, intersect, is.unsorted,
    lapply, mapply, match, mget, order, paste, pmax, pmax.int, pmin,
    pmin.int, rank, rbind, rownames, sapply, setdiff, sort, table,
    tapply, union, unique, unsplit, which.max, which.min


Attaching package: ‘S4Vectors’

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

    I, expand.grid, unname

Loading required package: IRanges Loading required package: GenomicRanges Loading required package: GenomeInfoDb Loading required package: SummarizedExperiment Loading required package: MatrixGenerics Loading required package: matrixStats

Attaching package: ‘MatrixGenerics’

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

    colAlls, colAnyNAs, colAnys, colAvgsPerRowSet, colCollapse,
    colCounts, colCummaxs, colCummins, colCumprods, colCumsums,
    colDiffs, colIQRDiffs, colIQRs, colLogSumExps, colMadDiffs,
    colMads, colMaxs, colMeans2, colMedians, colMins, colOrderStats,
    colProds, colQuantiles, colRanges, colRanks, colSdDiffs, colSds,
    colSums2, colTabulates, colVarDiffs, colVars, colWeightedMads,
    colWeightedMeans, colWeightedMedians, colWeightedSds,
    colWeightedVars, rowAlls, rowAnyNAs, rowAnys, rowAvgsPerColSet,
    rowCollapse, rowCounts, rowCummaxs, rowCummins, rowCumprods,
    rowCumsums, rowDiffs, rowIQRDiffs, rowIQRs, rowLogSumExps,
    rowMadDiffs, rowMads, rowMaxs, rowMeans2, rowMedians, rowMins,
    rowOrderStats, rowProds, rowQuantiles, rowRanges, rowRanks,
    rowSdDiffs, rowSds, rowSums2, rowTabulates, rowVarDiffs, rowVars,
    rowWeightedMads, rowWeightedMeans, rowWeightedMedians,
    rowWeightedSds, rowWeightedVars

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")'.


Attaching package: ‘Biobase’

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

    rowMedians

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

    anyMissing, rowMedians

Error: package or namespace load failed for ‘DESeq2’ in dyn.load(file, DLLpath = DLLpath, ...):  unable to load shared object '/Users/thusor/Library/R/x86_64/4.2/library/genefilter/libs/genefilter.so': dlopen(/Users/thusor/Library/R/x86_64/4.2/library/genefilter/libs/genefilter.so, 0x0006): Library not loaded: /usr/local/opt/gcc/lib/gcc/11/libgfortran.5.dylib   Referenced from: <7A0A9B4B-3511-3F56-87E6-8B1D36318737> /Users/thusor/Library/R/x86_64/4.2/library/genefilter/libs/genefilter.so Reason: tried: '/usr/local/opt/gcc/lib/gcc/11/libgfortran.5.dylib' (no such file), '/System/Volumes/Preboot/Cryptexes/OS/usr/local/opt/gcc/lib/gcc/11/libgfortran.5.dylib' (no such file), '/usr/local/opt/gcc/lib/gcc/11/libgfortran.5.dylib' (no such file), '/usr/local/Cellar/r/4.2.2/lib/R/lib/libgfortran.5.dylib' (no such file)```
DESeq2 apple-m1 • 308 views
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ATpoint ★ 2.1k
@atpoint-13662
Last seen 3 days ago
Germany

I would first restart R and see whether this goes away. Else, please precisely follow https://mac.r-project.org/tools/ and then reinstall DESeq2 and its dependencies. Please also use google and the search functions, M1-related Bioc questions are piling up here recently with solutions provided.

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1
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Thank you for your help and answer. I tried your solution and it helped.

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Also just a pointer: in the past week I have removed genefilter as a dependency of DESeq2, in release and devel branch.

We kept seeing these issues popping up so just removed the dependency altogether.

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