Question

Error in GRanges: could not find symbol "recursive" in environment of the generic function

5

Entering edit mode

deut13 ▴ 80

@deut13-8633

Last seen 5.3 years ago

Germany

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

granges chippeakanno • 7.7k views

ADD COMMENT • link updated 7.7 years ago by davide.porcellato ▴ 10 • written 7.7 years ago by deut13 ▴ 80

score 8 · Answer 1 · 2017-03-10

8

Entering edit mode

Martin Morgan 25k

@martin-morgan-1513

Last seen 4 months ago

United States

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 COMMENT • link 7.7 years ago Martin Morgan 25k

5

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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 REPLY • link 7.7 years ago Hervé Pagès 16k

0

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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 REPLY • link 7.7 years ago deut13 ▴ 80

0

Entering edit mode

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 REPLY • link 7.7 years ago Pengcheng Yang ▴ 60

2

Entering edit mode

yes reinstall

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

will help.

ADD REPLY • link 7.7 years ago • updated 7.6 years ago Ou, Jianhong ★ 1.3k

0

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

ADD REPLY • link 7.1 years ago lmolla ▴ 10

1

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

ADD REPLY • link 7.1 years ago Martin Morgan 25k

score 1 · Answer 2 · 2017-03-15

1

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davide.porcellato ▴ 10

@davideporcellato-12602

Last seen 7.7 years ago

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 COMMENT • link 7.7 years ago davide.porcellato ▴ 10

0

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

ADD REPLY • link 7.7 years ago Martin Morgan 25k

0

Entering edit mode

Hi,

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

Thanks

ADD REPLY • link 7.7 years ago davide.porcellato ▴ 10