[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

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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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