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Question: Error in GRanges: could not find symbol "recursive" in environment of the generic function
5
gravatar for deut13
7 months ago by
deut1350
Germany
deut1350 wrote:

Hi all,

I would be grateful for help on the following issue.

When running the function annotatePeakInBatch from package ChIPpeakAnno I get the following error:

Error in c(<S4 object of class "GRanges">, <S4 object of class "GRanges">,  : 
  could not find symbol "recursive" in environment of the generic function

This happens on a fresh R/Bioconductor installation.

When instead I install ChIPpeakAnno on an older R/Bioconductor version previously installed on the same machine and then run the same function it gives no problems. Here below is the session info of the installation giving the error.

Thanks!

> 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=English_United States.1252  LC_CTYPE=English_United States.1252   
[3] LC_MONETARY=English_United States.1252 LC_NUMERIC=C                          
[5] LC_TIME=English_United States.1252    

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

other attached packages:
 [1] ChIPpeakAnno_3.8.9   VennDiagram_1.6.17   futile.logger_1.4.3  GenomicRanges_1.26.3
 [5] GenomeInfoDb_1.10.3  Biostrings_2.42.1    XVector_0.14.0       IRanges_2.8.1       
 [9] S4Vectors_0.12.1     BiocGenerics_0.20.0 

loaded via a namespace (and not attached):
 [1] Rcpp_0.12.9                   AnnotationHub_2.6.4           BiocInstaller_1.24.0         
 [4] regioneR_1.6.2                GenomicFeatures_1.26.3        bitops_1.0-6                 
 [7] futile.options_1.0.0          tools_3.3.3                   zlibbioc_1.20.0              
[10] biomaRt_2.30.0                digest_0.6.12                 RSQLite_1.1-2                
[13] memoise_1.0.0                 lattice_0.20-34               BSgenome_1.42.0              
[16] Matrix_1.2-8                  graph_1.52.0                  shiny_1.0.0                  
[19] DBI_0.6                       yaml_2.1.14                   httr_1.2.1                   
[22] rtracklayer_1.34.2            ade4_1.7-5                    multtest_2.30.0              
[25] Biobase_2.34.0                R6_2.2.0                      AnnotationDbi_1.36.2         
[28] XML_3.98-1.5                  survival_2.40-1               RBGL_1.50.0                  
[31] BiocParallel_1.8.1            limma_3.30.12                 seqinr_3.3-3                 
[34] idr_1.2                       ensembldb_1.6.2               GO.db_3.4.0                  
[37] lambda.r_1.1.9                matrixStats_0.51.0            htmltools_0.3.5              
[40] Rsamtools_1.26.1              splines_3.3.3                 MASS_7.3-45                  
[43] GenomicAlignments_1.10.0      SummarizedExperiment_1.4.0    xtable_1.8-2                 
[46] mime_0.5                      interactiveDisplayBase_1.12.0 httpuv_1.3.3                 
[49] RCurl_1.95-4.8               
 
 

 

 

ADD COMMENTlink modified 7 months ago by davide.porcellato10 • written 7 months ago by deut1350
8
gravatar for Martin Morgan
7 months ago by
Martin Morgan ♦♦ 20k
United States
Martin Morgan ♦♦ 20k wrote:

See here A: Combining RangedData objects is broken (IRanges 2.8.1 with R version 3.3.3 RC) for a similar problem -- reinstall your Bioconductor packages.

 

ADD COMMENTlink written 7 months ago by Martin Morgan ♦♦ 20k
5

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.

H.

ADD REPLYlink modified 7 months ago • written 7 months ago by Hervé Pagès ♦♦ 12k

Thank you all!

I had searched online but missed the other post.

After reinstalling from source the issue seems solved. (Before I had to remove the installed packages and then also manually delete what remained in the library folders - without this it was giving a problem in copying the .dll files during package installation)

ADD REPLYlink modified 7 months ago • written 7 months ago by deut1350

Hi Herve Pages, I cann't reinstall these packages from source on my Win7 system. As you have suggested, I will switch to the R 3.3.2 version. Thank you.

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’
ADD REPLYlink written 7 months ago by Pengcheng Yang50
2

yes reinstall

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

will help.

ADD REPLYlink modified 6 months ago • written 7 months ago by Ou, Jianhong1000

any solutions if I have Mac OS X 10.9 (Mavericks) ; can not update R in this case

ADD REPLYlink written 10 days ago by lmolla0
1

Did you try to reinstall the packages suggested by Jianhong? Does BiocInstaller::biocValid() point to additional problems that you can address?

ADD REPLYlink written 10 days ago by Martin Morgan ♦♦ 20k
1
gravatar for davide.porcellato
7 months ago by
davide.porcellato10 wrote:

Hi,

I have the same problem as above but with the package DECIPHER. When I run these 2 functions AlignSeqs and AlignTranslation I get this error. I have been using this two functions for a while without problem. The functions stopped to work after I upgraded a series of packages from Bioconductor. I have updated all the packages (from source) and still get the same error. 

 

The two errors I get for the 2 functions are: 

ali <- AlignTranslation(seqs,readingFrame=NA,asAAStringSet = F,verbose=F)

Error in c(x, value) : 

  could not find symbol "recursive" in environment of the generic function”

 

and 

 

ali<- AlignSeqs(seqs)

Error in c(x@pool, y@pool) : 

  could not find symbol "recursive" in environment of the generic function”

 

Here is my session.Info()

DECIPHER_2.2.0      RSQLite_1.1-2       Biostrings_2.42.1   XVector_0.14.0      IRanges_2.8.1      

S4Vectors_0.12.1    BiocGenerics_0.20.0​

 

Thanks for any help

ADD COMMENTlink written 7 months ago by davide.porcellato10

Please provide your full sessionInfo() (after the error occurs) and the command that you used to update your packages.

ADD REPLYlink written 7 months ago by Martin Morgan ♦♦ 20k

Hi,

I reinstalled most (if not all) of the packages from Bioconductor from source and now the functions works. 

Thanks 

 

ADD REPLYlink written 7 months ago by davide.porcellato10
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