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

[Raymond Cavalcante]

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

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