Question: Biostrings: revComp error: Not compatible with STRSXP
0
gravatar for camille.4nier
5 weeks ago by
camille.4nier0 wrote:

Dear Bioconductor, 

I'm experiencing somewhat of a trouble with Biostrings. It works in one session and not in the other. So here I am, with, I hope, a reproducible example.

This is my first posting, I hope it follows more or less the Posting Guide. 

Thank you for your help !

So, in the first case, Biostrings works like a charm:

> require("Biostrings")
> packageVersion("Biostrings")
[1] ‘2.50.1’
> example<-DNAString("AGAGTTTGAT")
> reverse(example)
  10-letter "DNAString" instance
seq: TAGTTTGAGA
> complement(example)
  10-letter "DNAString" instance
seq: TCTCAAACTA
> reverseComplement(example)
  10-letter "DNAString" instance
seq: ATCAAACTCT

R version 3.5.1 (2018-07-02)
Platform: x86_64-w64-mingw32/x64 (64-bit)
Running under: Windows >= 8 x64 (build 9200)

Matrix products: default

locale:
[1] LC_COLLATE=English_United Kingdom.1252  LC_CTYPE=English_United Kingdom.1252    LC_MONETARY=English_United Kingdom.1252
[4] LC_NUMERIC=C                            LC_TIME=English_United Kingdom.1252    

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

other attached packages:
[1] Biostrings_2.50.1   XVector_0.22.0      IRanges_2.16.0      S4Vectors_0.20.1    BiocGenerics_0.28.0

loaded via a namespace (and not attached):
[1] zlibbioc_1.28.0 compiler_3.5.1  tools_3.5.1    

 

 

In the second case, less so: 

> example<-DNAString("AGAGTTTGAT")
> reverse(example)
  10-letter "DNAString" instance
seq: TAGTTTGAGA
> complement(example)
1 DNA sequence in binary format stored in a vector.
Sequence length: 10 
Base composition:
  a   c   g   t 
NaN NaN NaN NaN 
(Total: 10 bases)
> reverseComplement(example)
Error in revComp(nuc.sequences, reverse) : 
  Not compatible with STRSXP: [type=S4].

> sessionInfo()
R version 3.5.1 (2018-07-02)
Platform: x86_64-w64-mingw32/x64 (64-bit)
Running under: Windows >= 8 x64 (build 9200)

Matrix products: default

locale:
[1] LC_COLLATE=English_United Kingdom.1252  LC_CTYPE=English_United Kingdom.1252    LC_MONETARY=English_United Kingdom.1252
[4] LC_NUMERIC=C                            LC_TIME=English_United Kingdom.1252    

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

other attached packages:
 [1] microseq_1.2.2              dplyr_0.7.8                 microbiome_1.4.2            phangorn_2.4.0             
 [5] ape_5.2                     phyloseq_1.26.0             ShortRead_1.40.0            GenomicAlignments_1.18.0   
 [9] SummarizedExperiment_1.12.0 DelayedArray_0.8.0          matrixStats_0.54.0          Biobase_2.42.0             
[13] Rsamtools_1.34.0            GenomicRanges_1.34.0        GenomeInfoDb_1.18.1         BiocParallel_1.16.2        
[17] dada2_1.10.0                Rcpp_1.0.0                  gridExtra_2.3               ggplot2_3.1.0              
[21] knitr_1.20                  Biostrings_2.50.1           XVector_0.22.0              IRanges_2.16.0             
[25] S4Vectors_0.20.1            BiocGenerics_0.28.0        

loaded via a namespace (and not attached):
 [1] tidyr_0.8.2            bit64_0.9-7            jsonlite_1.6           splines_3.5.1          foreach_1.4.4         
 [6] RcppParallel_4.4.1     assertthat_0.2.0       BiocManager_1.30.4     latticeExtra_0.6-28    blob_1.1.1            
[11] GenomeInfoDbData_1.2.0 pillar_1.3.0           lattice_0.20-35        quadprog_1.5-5         glue_1.3.0            
[16] RColorBrewer_1.1-2     colorspace_1.3-2       Matrix_1.2-14          plyr_1.8.4             pkgconfig_2.0.2       
[21] zlibbioc_1.28.0        purrr_0.2.5            scales_1.0.0           tibble_1.4.2           mgcv_1.8-24           
[26] withr_2.1.2            lazyeval_0.2.1         survival_2.42-3        magrittr_1.5           crayon_1.3.4          
[31] nlme_3.1-137           MASS_7.3-50            hwriter_1.3.2          vegan_2.5-3            tools_3.5.1           
[36] data.table_1.11.8      stringr_1.3.1          Rhdf5lib_1.4.2         munsell_0.5.0          cluster_2.0.7-1       
[41] bindrcpp_0.2.2         ade4_1.7-13            compiler_3.5.1         rlang_0.3.0.1          rhdf5_2.26.0          
[46] grid_3.5.1             RCurl_1.95-4.11        iterators_1.0.10       biomformat_1.10.0      igraph_1.2.2          
[51] bitops_1.0-6           gtable_0.2.0           codetools_0.2-15       multtest_2.38.0        DBI_1.0.0             
[56] reshape2_1.4.3         R6_2.3.0               bit_1.1-14             fastmatch_1.1-0        bindr_0.1.1           
[61] permute_0.9-4          stringi_1.2.4          tidyselect_0.2.5 
ADD COMMENTlink written 5 weeks ago by camille.4nier0

You have a lot more packages loaded in the second session, and I would guess that one of these has functions called complement and reverseComplement and these are over-riding the versions present in Biostrings.

You could take a look at the conflicted package (https://conflicted.r-lib.org/) which tries to help you identify when two packages will conflict like this, and suggests some ways to work around it.

ADD REPLYlink modified 5 weeks ago • written 5 weeks ago by Mike Smith3.2k

Thank you very much for your quick answer. A wonderful tool that is ! It works again. 

ADD REPLYlink written 4 weeks ago by camille.4nier0
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