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