Reason: image not found Error: package GenomeInfoDb could not be loaded
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adam.cribbs ▴ 10
@adamcribbs-11651
Last seen 4.1 years ago

No sure if this is the best place to ask this question or if its a conda related issue. However, after installing a conda environment and then installing the bioconda-deseq2 package, I am profiling some code on a mac (runs ok on linux) and I am getting issues with shared objects:

 

> 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, basename, cbind, colMeans,

    colnames, colSums, dirname, 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

Error: package or namespace load failed for ‘GenomeInfoDb’ in dyn.load(file, DLLpath = DLLpath, ...):

 unable to load shared object '/Users/adamc/anaconda2/envs/showcase3/lib/R/library/bitops/libs/bitops.so':

  dlopen(/Users/adamc/anaconda2/envs/showcase3/lib/R/library/bitops/libs/bitops.so, 6): Library not loaded: @rpath/libintl.9.dylib

  Referenced from: /Users/adamc/anaconda2/envs/showcase3/lib/R/library/bitops/libs/bitops.so

  Reason: image not found

Error: package ‘GenomeInfoDb’ could not be loaded

> sessionInfo()

R version 3.4.1 (2017-06-30)

Platform: x86_64-apple-darwin14.5.0 (64-bit)

Running under: macOS High Sierra 10.13.6


Matrix products: default

BLAS: /System/Library/Frameworks/Accelerate.framework/Versions/A/Frameworks/vecLib.framework/Versions/A/libBLAS.dylib

LAPACK: /System/Library/Frameworks/Accelerate.framework/Versions/A/Frameworks/vecLib.framework/Versions/A/libLAPACK.dylib


locale:

[1] en_GB.UTF-8/en_GB.UTF-8/en_GB.UTF-8/C/en_GB.UTF-8/en_GB.UTF-8


attached base packages:

[1] parallel  stats4    stats     graphics  grDevices utils     datasets 

[8] methods   base     


other attached packages:

[1] IRanges_2.14.12     S4Vectors_0.18.3    BiocGenerics_0.26.0


loaded via a namespace (and not attached):

[1] compiler_3.4.1

Thanks

deseq2 conda • 950 views
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@martin-morgan-1513
Last seen 7 days ago
United States

Did you use biocLite() or BiocManager::install() to install packages in your conda installation? I think that you must opt fully for conda (and live with outdated versions and perhaps some packages that are not available) or fully for installation 'by hand' for the reasons described at https://github.com/conda-forge/r-base-feedstock/issues/55

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adam.cribbs ▴ 10
@adamcribbs-11651
Last seen 4.1 years ago

I used conda exclusively on a clean environment. I will try conda create --name deseq2 bioconductor-deseq2 gcc as suggested by the linked issue.

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Entering edit mode

I probably didn't read the error message carefully enough. It looks like your conda environment doesn't have libintl.9.dylib. It isn't obvious from google how to install this in conda, other than through indirectly through some other package. Probably more help available in conda forums. Sorry for misleading.

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