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Question: Fail to load "MotifDb" package
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gravatar for Pengcheng Yang
8 months ago by
China
Pengcheng Yang50 wrote:

Hi all,

I have successfully installed "MotifDb" package,but failed to load it, and got the following error message. After a while searching, It may be caused by some R package that not updated to the newest version. However, I have upgraded all the packages.

Thank you!

=====================

> library(MotifDb)
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, xtabs

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

    anyDuplicated, append, as.data.frame, cbind, colnames, 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, rownames, sapply, setdiff, sort, table,
    tapply, union, unique, unsplit, which, which.max, which.min

Loading required package: S4Vectors
Loading required package: stats4

Attaching package: ‘S4Vectors’

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

    colMeans, colSums, expand.grid, rowMeans, rowSums

Loading required package: IRanges
Loading required package: Biostrings
Loading required package: XVector
Error : .onLoad failed in loadNamespace() for 'MotifDb', details:
  call: c(values, x)
  error: could not find symbol "recursive" in environment of the generic function
Error: package or namespace load failed for ‘MotifDb’

> sessionInfo()
R version 3.3.3 (2017-03-06)
Platform: x86_64-w64-mingw32/x64 (64-bit)
Running under: Windows 7 x64 (build 7601) Service Pack 1

locale:
[1] LC_COLLATE=Chinese (Simplified)_People's Republic of China.936 
[2] LC_CTYPE=Chinese (Simplified)_People's Republic of China.936   
[3] LC_MONETARY=Chinese (Simplified)_People's Republic of China.936
[4] LC_NUMERIC=C                                                   
[5] LC_TIME=Chinese (Simplified)_People's Republic of China.936    

attached base packages:
[1] stats4    parallel  stats     graphics  grDevices utils     datasets  methods  
[9] base     

other attached packages:
[1] rJava_0.9-8          Biostrings_2.42.1    XVector_0.14.0       IRanges_2.8.1       
[5] S4Vectors_0.12.1     BiocGenerics_0.20.0  BiocInstaller_1.24.0

loaded via a namespace (and not attached):
 [1] GenomicRanges_1.26.3       zlibbioc_1.20.0            GenomicAlignments_1.10.0  
 [4] BiocParallel_1.8.1         lattice_0.20-34            GenomeInfoDb_1.10.3       
 [7] tools_3.3.3                SummarizedExperiment_1.4.0 grid_3.3.3                
[10] Biobase_2.34.0             Matrix_1.2-8               rtracklayer_1.34.2        
[13] bitops_1.0-6               RCurl_1.95-4.8             Rsamtools_1.26.1          
[16] XML_3.98-1.5     

ADD COMMENTlink modified 8 months ago by Paul Shannon360 • written 8 months ago by Pengcheng Yang50

The following solution come from: C: Error in GRanges: could not find symbol "recursive" in environment of the generi

You'll actually have to reinstall from source i.e. with:

biocLite(c("BiocGenerics", "S4Vectors", "IRanges", "GenomicRanges"),
         type="source")

which won't work if your system is not set up for doing this. Our Windows and Mac binary packages are not fully compatible with R 3.3.3 yet. We're working on it.

In the meantime, if you're on Windows or Mac, and don't know how to set up your system to install from source, the recommendation is to stick to R 3.3.2.
ADD REPLYlink written 8 months ago by Pengcheng Yang50
3
gravatar for Paul Shannon
8 months ago by
Paul Shannon360
Paul Shannon360 wrote:

Pengcheng Yang,

Sorry you encountered trouble with MotifDb.  

The same error, with a solution proposed, is reported here:  Error in GRanges: could not find symbol "recursive" in environment of the generic function

Could you give that a try?

 - Paul

 

ADD COMMENTlink written 8 months ago by Paul Shannon360

Hi Paul Shanno,

Thank you for your reply and the provided information. I have tried the solution and successfully loaded the MotifDb library under R 3.3.2 version.

Pengcheng

ADD REPLYlink modified 8 months ago • written 8 months ago by Pengcheng Yang50
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