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

Thu Oct 26 23:37:25 CEST 2017

Hi Martin,

A ha! Thank you for pointing that out. Not sure how that space got in there, but I’ll remove it and hopefully it’ll clear the error. Odd about the reproducibility though…

Thanks again,
Raymond

> On Oct 26, 2017, at 17:34, Martin Morgan <martin.morgan at roswellpark.org> wrote:
> 
> On 10/23/2017 09:22 AM, Raymond Cavalcante wrote:
>> 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 '*'.
> 
> I'm not able to reproduce this off the build system either, but the problem is the space after the strand '- ' instead of '-' in the second line,
> 
> > r_file = system.file('extdata', 'test_read_multiple_data_nohead.bed', package='annotatr')
> > readLines(r_file)
> [1] "chr1\t10800\t10900\tA\t87\t+\t10e-4\t100\t13\tY"
> [2] "chr1\t11000\t11100\tA\t45\t- \t1e-6\t100\t55\tN"
> [3] "chr1\t27800\t28800\tA\t34\t-\t0.04\t41\t7\tY"
> [4] "chr1\t29000\t29300\tB\t62\t+\t0.001\t95\t33\tY"
> 
> Maybe Michael has some insight...?
> 
> Martin
> 
> 
>> 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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