Hello all, I’m getting some CHECK errors in the examples and tests for the annotatr package (http://bioconductor.org/checkResults/devel/bioc-LATEST/annotatr/ <http://bioconductor.org/checkResults/devel/bioc-LATEST/annotatr/>) that I cannot reproduce using the bioconductor/devel_core2 Docker image + most up-to-date packages. I think the issue is coming from rtracklayer while reading in a BED (or BED-like) file that has '.' in the strand column instead of '+', '-', or '*'.
Here is the error on the build system for all three platforms: > Running examples in ‘annotatr-Ex.R’ failed > The error most likely occurred in: > > > base::assign(".ptime", proc.time(), pos = "CheckExEnv") > > ### Name: annotate_regions > > ### Title: A function to intersect user region data with annotation data > > ### Aliases: annotate_regions > > > > ### ** Examples > > > > r_file = system.file('extdata', 'test_read_multiple_data_nohead.bed', > > package='annotatr') > > extraCols = c(pval = 'numeric', mu1 = 'integer', mu0 = 'integer', > > diff_exp = 'character') > > r = read_regions(con = r_file, extraCols = extraCols, rename_score = > > 'coverage') > Error in .local(x, ...) : strand values must be in '+' '-' '*' > Calls: read_regions ... GenomicData -> normStrand -> strand -> strand -> > .local > Execution halted Below is my sessionInfo() for the Docker image based on the https://hub.docker.com/r/bioconductor/devel_core2/ <https://hub.docker.com/r/bioconductor/devel_core2/> image. I suppose I could change all of my example data to use '*' for the strand, but many peak callers (macs2 being one of the most popular) use the '.' convention for no strand in their BED output, and I think rtracklayer should respect this. Thanks, Raymond > > sessionInfo() > R version 3.4.1 (2017-06-30) > Platform: x86_64-pc-linux-gnu (64-bit) > Running under: Debian GNU/Linux 9 (stretch) > > Matrix products: default > BLAS/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=C > [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] stats graphics grDevices utils datasets methods base > > other attached packages: > [1] annotatr_1.3.2 BiocInstaller_1.27.6 > > loaded via a namespace (and not attached): > [1] Biobase_2.37.2 > [2] httr_1.3.1 > [3] regioneR_1.9.2 > [4] org.Rn.eg.db_3.4.2 > [5] bit64_0.9-7 > [6] AnnotationHub_2.9.21 > [7] TxDb.Mmusculus.UCSC.mm10.knownGene_3.4.0 > [8] shiny_1.0.5 > [9] assertthat_0.2.0 > [10] interactiveDisplayBase_1.15.0 > [11] stats4_3.4.1 > [12] blob_1.1.0 > [13] BSgenome_1.45.3 > [14] GenomeInfoDbData_0.99.1 > [15] Rsamtools_1.29.1 > [16] yaml_2.1.14 > [17] progress_1.1.2 > [18] RSQLite_2.0 > [19] lattice_0.20-35 > [20] glue_1.1.1 > [21] digest_0.6.12 > [22] GenomicRanges_1.29.15 > [23] XVector_0.17.2 > [24] colorspace_1.3-2 > [25] htmltools_0.3.6 > [26] httpuv_1.3.5 > [27] Matrix_1.2-11 > [28] plyr_1.8.4 > [29] TxDb.Hsapiens.UCSC.hg38.knownGene_3.4.0 > [30] XML_3.98-1.9 > [31] pkgconfig_2.0.1 > [32] TxDb.Rnorvegicus.UCSC.rn6.refGene_3.4.1 > [33] biomaRt_2.33.4 > [34] org.Mm.eg.db_3.4.2 > [35] zlibbioc_1.23.0 > [36] xtable_1.8-2 > [37] scales_0.5.0 > [38] TxDb.Rnorvegicus.UCSC.rn4.ensGene_3.2.2 > [39] org.Dm.eg.db_3.4.2 > [40] BiocParallel_1.11.13 > [41] tibble_1.3.4 > [42] IRanges_2.11.19 > [43] ggplot2_2.2.1 > [44] SummarizedExperiment_1.7.10 > [45] GenomicFeatures_1.29.13 > [46] BiocGenerics_0.23.4 > [47] lazyeval_0.2.0 > [48] magrittr_1.5 > [49] mime_0.5 > [50] memoise_1.1.0 > [51] tools_3.4.1 > [52] prettyunits_1.0.2 > [53] hms_0.3 > [54] org.Hs.eg.db_3.4.2 > [55] matrixStats_0.52.2 > [56] stringr_1.2.0 > [57] S4Vectors_0.15.14 > [58] munsell_0.4.3 > [59] DelayedArray_0.3.21 > [60] AnnotationDbi_1.39.4 > [61] bindrcpp_0.2 > [62] TxDb.Rnorvegicus.UCSC.rn5.refGene_3.4.2 > [63] Biostrings_2.45.4 > [64] compiler_3.4.1 > [65] GenomeInfoDb_1.13.5 > [66] rlang_0.1.2 > [67] grid_3.4.1 > [68] RCurl_1.95-4.8 > [69] TxDb.Dmelanogaster.UCSC.dm6.ensGene_3.4.1 > [70] bitops_1.0-6 > [71] gtable_0.2.0 > [72] DBI_0.7 > [73] reshape2_1.4.2 > [74] R6_2.2.2 > [75] GenomicAlignments_1.13.6 > [76] dplyr_0.7.4 > [77] rtracklayer_1.37.3 > [78] bit_1.1-12 > [79] bindr_0.1 > [80] readr_1.1.1 > [81] stringi_1.1.5 > [82] TxDb.Hsapiens.UCSC.hg19.knownGene_3.2.2 > [83] parallel_3.4.1 > [84] Rcpp_0.12.13 > [85] TxDb.Mmusculus.UCSC.mm9.knownGene_3.2.2 > [86] TxDb.Dmelanogaster.UCSC.dm3.ensGene_3.2.2 [[alternative HTML version deleted]] _______________________________________________ Bioc-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/bioc-devel