Hi,

I was getting an error with a simple Biostring function. Here is the code, error and session info. Am I using some outdated package?

many thanks!

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

> library(Biostrings)
> 
> tdna <- DNAString("TGCGATGCGCACG")
> print(tdna)
  13-letter "DNAString" instance
seq: TGCGATGCGCACG
> 
> ti <- matchPDict(DNAStringSet("GC","CG"),tdna)
Error in .normargSEW(start, "start") : 
  'start' must be a vector of integers


> sessionInfo()
R version 3.4.3 (2017-11-30)
Platform: x86_64-apple-darwin15.6.0 (64-bit)
Running under: macOS High Sierra 10.13.2

Matrix products: default
BLAS: /System/Library/Frameworks/Accelerate.framework/Versions/A/Frameworks/vecLib.framework/Versions/A/libBLAS.dylib
LAPACK: /Library/Frameworks/R.framework/Versions/3.4/Resources/lib/libRlapack.dylib

locale:
[1] en_US.UTF-8/en_US.UTF-8/en_US.UTF-8/C/en_US.UTF-8/en_US.UTF-8

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

other attached packages:
 [1] BSgenome.Hsapiens.UCSC.hg38_1.4.1        annotatr_1.4.1                          
 [3] TxDb.Mmulatta.UCSC.rheMac8.refGene_3.4.2 org.Mmu.eg.db_3.5.0                     
 [5] BSgenome.Mmulatta.UCSC.rheMac8_1.4.2     dplyr_0.7.4                             
 [7] regioneR_1.10.0                          BSgenome_1.46.0                         
 [9] rtracklayer_1.38.3                       Biostrings_2.46.0                       
[11] XVector_0.18.0                           memoise_1.1.0                           
[13] Gviz_1.22.3                              TxDb.Hsapiens.UCSC.hg38.knownGene_3.4.0 
[15] GenomicFeatures_1.30.3                   hash_2.2.6                              
[17] biomaRt_2.34.2                           topGO_2.30.1                            
[19] SparseM_1.77                             GO.db_3.5.0                             
[21] graph_1.56.0                             org.Hs.eg.db_3.5.0                      
[23] AnnotationDbi_1.40.0                     reutils_0.2.3                           
[25] XML_3.98-1.10                            DSS_2.26.0                              
[27] bsseq_1.14.0                             SummarizedExperiment_1.8.1              
[29] DelayedArray_0.4.1                       matrixStats_0.53.1                      
[31] Biobase_2.38.0                           GenomicRanges_1.30.3                    
[33] GenomeInfoDb_1.14.0                      IRanges_2.12.0                          
[35] S4Vectors_0.16.0                         BiocGenerics_0.24.0                     
[37] R2HTML_2.3.2                             BiocInstaller_1.28.0                    

loaded via a namespace (and not attached):
 [1] backports_1.1.2                           TxDb.Dmelanogaster.UCSC.dm6.ensGene_3.4.1
 [3] Hmisc_4.1-1                               AnnotationHub_2.10.1                     
 [5] plyr_1.8.4                                lazyeval_0.2.1                           
 [7] BiocParallel_1.12.0                       ggplot2_2.2.1                            
 [9] digest_0.6.15                             ensembldb_2.2.2                          
[11] htmltools_0.3.6                           magrittr_1.5                             
[13] checkmate_1.8.5                           cluster_2.0.7-1                          
[15] limma_3.34.9                              org.Rn.eg.db_3.5.0                       
[17] readr_1.1.1                               R.utils_2.6.0                            
[19] prettyunits_1.0.2                         colorspace_1.3-2                         
[21] blob_1.1.1                                RCurl_1.95-4.10                          
[23] org.Mm.eg.db_3.5.0                        TxDb.Hsapiens.UCSC.hg19.knownGene_3.2.2  
[25] bindr_0.1.1                               survival_2.41-3                          
[27] VariantAnnotation_1.24.5                  glue_1.2.0                               
[29] gtable_0.2.0                              zlibbioc_1.24.0                          
[31] TxDb.Rnorvegicus.UCSC.rn5.refGene_3.4.2   scales_0.5.0                             
[33] DBI_0.8                                   org.Dm.eg.db_3.5.0                       
[35] TxDb.Mmusculus.UCSC.mm9.knownGene_3.2.2   Rcpp_0.12.16                             
[37] xtable_1.8-2                              progress_1.1.2                           
[39] htmlTable_1.11.2                          foreign_0.8-69                           
[41] bit_1.1-12                                Formula_1.2-2                            
[43] htmlwidgets_1.0                           httr_1.3.1                               
[45] RColorBrewer_1.1-2                        acepack_1.4.1                            
[47] pkgconfig_2.0.1                           R.methodsS3_1.7.1                        
[49] nnet_7.3-12                               locfit_1.5-9.1                           
[51] rlang_0.2.0                               reshape2_1.4.3                           
[53] munsell_0.4.3                             tools_3.4.3                              
[55] RSQLite_2.1.0                             stringr_1.3.0                            
[57] yaml_2.1.18                               knitr_1.20                               
[59] bit64_0.9-7                               AnnotationFilter_1.2.0                   
[61] bindrcpp_0.2.2                            mime_0.5                                 
[63] TxDb.Rnorvegicus.UCSC.rn4.ensGene_3.2.2   R.oo_1.21.0                              
[65] compiler_3.4.3                            rstudioapi_0.7                           
[67] curl_3.2                                  interactiveDisplayBase_1.16.0            
[69] tibble_1.4.2                              TxDb.Rnorvegicus.UCSC.rn6.refGene_3.4.1  
[71] stringi_1.1.7                             lattice_0.20-35                          
[73] ProtGenerics_1.10.0                       Matrix_1.2-14                            
[75] permute_0.9-4                             pillar_1.2.1                             
[77] data.table_1.10.4-3                       bitops_1.0-6                             
[79] TxDb.Mmusculus.UCSC.mm10.knownGene_3.4.0  httpuv_1.3.6.2                           
[81] R6_2.2.2                                  latticeExtra_0.6-28                      
[83] RMySQL_0.10.14                            gridExtra_2.3                            
[85] dichromat_2.0-0                           gtools_3.5.0                             
[87] assertthat_0.2.0                          GenomicAlignments_1.14.2                 
[89] Rsamtools_1.30.0                          GenomeInfoDbData_1.0.0                   
[91] hms_0.4.2                                 rpart_4.1-13                             
[93] TxDb.Dmelanogaster.UCSC.dm3.ensGene_3.2.2 biovizBase_1.26.0                        
[95] shiny_1.0.5                               base64enc_0.1-3  

The DNAStringSet should be initialized with a _vector_ c("GC", "CG"), so

DNAStringSet(c("GC","CG"))

I didn't see this at first so did

> ti <- matchPDict(DNAStringSet("GC","CG"),tdna)
Error in .normargSEW(start, "start") : 
  'start' must be a vector of integers> traceback()
> traceback()
12: stop("'", argname, "' must be a vector of integers")
11: .normargSEW(start, "start")
10: solveUserSEW(length(ans_xvector), start = start, end = end, width = width, 
        rep.refwidths = TRUE)
9: .oneSeqToXStringSet(seqtype, x, start, end, width, use.names)
8: .charToXStringSet(seqtype, x, start, end, width, use.names)
7: XStringSet("DNA", x, start = start, end = end, width = width, 
       use.names = use.names)
6: XStringSet("DNA", x, start = start, end = end, width = width, 
       use.names = use.names)
5: DNAStringSet("GC", "CG")
4: is(pdict, "PDict")
3: .matchPDict(pdict, subject, max.mismatch, min.mismatch, with.indels, 
       fixed, algorithm, verbose)
2: matchPDict(DNAStringSet("GC", "CG"), tdna)
1: matchPDict(DNAStringSet("GC", "CG"), tdna)

which is the 'call stack' at the time of the error, and at level 5 we can see that it's just the call to DNAStringSet() that causes problems.