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camille.4nier
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@camille4nier-18765
Last seen 5.8 years ago
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
You have a lot more packages loaded in the second session, and I would guess that one of these has functions called
complement
andreverseComplement
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.
Thank you very much for your quick answer. A wonderful tool that is ! It works again.