After updating my R version to 3.4.0 on a mac, after successfully re-installing sundry bioconductor modules, including DESeq2, when I load DESeq2 I get the following:
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, cbind, colMeans, colnames, colSums, do.call, duplicated, eval, evalq, Filter, Find, get, grep, grepl, intersect, is.unsorted, lapply, lengths, Map, mapply, match,
mget, order, paste, pmax, pmax.int, pmin, pmin.int, Position, rank, rbind, Reduce, rowMeans, rownames, rowSums, 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
Attaching package: ‘DelayedArray’
The following objects are masked from ‘package:matrixStats’:
colMaxs, colMins, colRanges, rowMaxs, rowMins, rowRanges
The following object is masked from ‘package:base’:
apply
Error: package or namespace load failed for ‘DESeq2’ in dyn.load(file, DLLpath = DLLpath, ...):
unable to load shared object '/Users/adamfreedman/Library/R/3.4/library/genefilter/libs/genefilter.so':
dlopen(/Users/adamfreedman/Library/R/3.4/library/genefilter/libs/genefilter.so, 6): Library not loaded: /usr/local/gfortran/lib/libgfortran.3.dylib
Referenced from: /Users/adamfreedman/Library/R/3.4/library/genefilter/libs/genefilter.so
Reason: image not found
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Any idea what's going on here?
Thanks,
Adam Freedman
Actually, it looks like I'm having the same problem with edgeR too. Both ~/Library/R/3.4/library/edgeR and Library/R/3.4/library/DESeq2 directories exist, and they aren't empty either. And the error messages indicate the problem is not, as with a previous post, trying to load from a library directory from the older version. I have not seen the problem with other bioconductor modules installed on 3.4 thus far.
Can you post sessionInfo() ?
This is sometimes helpful for resolving problems.