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

Thu Oct 26 23:34:56 CEST 2017

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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