[Bioc-devel] "chartr" method for MaskedXString objects with active masks not ready yet Please complain!

[Tim Triche, Jr.]

Hey I'm just doing what I'm told... any easy/obvious thing for me to fix?
I can submit a patch if I know what style is expected... I do need this
sort of functionality, as it happens.

R> as.character(stubbed[1])
                      ANKMY1
"chr2:240418839-242500275:-"

R> CGmasked <- maskMotif(getSeq(Hsapiens,
                         stubbed)[[1]],
                         "CG")

R> chartr("C", "T", CGmasked)
Error in chartr("C", "T", CGmasked) :
  "chartr" method for MaskedXString objects with active masks not ready yet
  Please complain!

R> sessionInfo()
R version 3.4.1 (2017-06-30)
Platform: x86_64-pc-linux-gnu (64-bit)
Running under: Ubuntu 17.04

Matrix products: default
BLAS: /usr/lib/openblas-base/libblas.so.3
LAPACK: /usr/lib/libopenblasp-r0.2.19.so

locale:
 [1] LC_CTYPE=en_US.UTF-8       LC_NUMERIC=C
 [3] LC_TIME=en_US.UTF-8        LC_COLLATE=en_US.UTF-8
 [5] LC_MONETARY=en_US.UTF-8    LC_MESSAGES=en_US.UTF-8
 [7] LC_PAPER=en_US.UTF-8       LC_NAME=C
 [9] LC_ADDRESS=C               LC_TELEPHONE=C
[11] LC_MEASUREMENT=en_US.UTF-8 LC_IDENTIFICATION=C

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

other attached packages:
 [1] BSgenome.Hsapiens.UCSC.hg19_1.4.0
 [2] BSgenome_1.45.3
 [3] Biostrings_2.45.4
 [4] XVector_0.17.1
 [5] Homo.sapiens_1.3.1
 [6] TxDb.Hsapiens.UCSC.hg19.knownGene_3.2.2
 [7] GO.db_3.4.1
 [8] OrganismDbi_1.19.0
 [9] BiocInstaller_1.27.4
[10] org.Hs.eg.db_3.4.1
[11] GenomicFeatures_1.29.11
[12] AnnotationDbi_1.39.3
[13] Biobase_2.37.2
[14] rtracklayer_1.37.3
[15] GenomicRanges_1.29.14
[16] GenomeInfoDb_1.13.4
[17] IRanges_2.11.17
[18] S4Vectors_0.15.8
[19] BiocGenerics_0.23.1
[20] nvimcom_0.9-28
[21] skeletor_1.0.4
[22] magrittr_1.5
[23] gtools_3.5.0
[24] useful_1.2.3
[25] ggplot2_2.2.1.9000
[26] purrr_0.2.3
[27] knitr_1.17

loaded via a namespace (and not attached):
 [1] httr_1.3.1                 bit64_0.9-7
 [3] assertthat_0.2.0           RBGL_1.53.0
 [5] blob_1.1.0                 GenomeInfoDbData_0.99.1
 [7] Rsamtools_1.29.1           progress_1.1.2
 [9] RSQLite_2.0                lattice_0.20-35
[11] glue_1.1.1                 digest_0.6.12
[13] colorspace_1.3-2           Matrix_1.2-11
[15] plyr_1.8.4                 XML_3.98-1.9
[17] pkgconfig_2.0.1            devtools_1.13.3
[19] biomaRt_2.33.4             zlibbioc_1.23.0
[21] scales_0.5.0               BiocParallel_1.11.8
[23] git2r_0.19.0               tibble_1.3.4
[25] withr_2.0.0                SummarizedExperiment_1.7.9
[27] lazyeval_0.2.0             memoise_1.1.0
[29] xml2_1.1.1                 graph_1.55.0
[31] tools_3.4.1                prettyunits_1.0.2
[33] matrixStats_0.52.2         stringr_1.2.0
[35] munsell_0.4.3              DelayedArray_0.3.20
[37] bindrcpp_0.2               compiler_3.4.1
[39] rlang_0.1.2                grid_3.4.1
[41] RCurl_1.95-4.8             tcltk_3.4.1
[43] bitops_1.0-6               gtable_0.2.0
[45] curl_2.8.1                 DBI_0.7
[47] roxygen2_6.0.1             R6_2.2.2
[49] GenomicAlignments_1.13.6   dplyr_0.7.3
[51] bit_1.1-12                 bindr_0.1
[53] commonmark_1.4             stringi_1.1.5
[55] Rcpp_0.12.12



--t

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