[Bioc-devel] Cannot reproduce Bioc build server errors for annotatr package
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