[Bioc-devel] GenomicScores: irreproducible build error caused by gwascat

Martin Morgan mtmorg@n@b|oc @end|ng |rom gm@||@com
Fri Jun 5 13:34:34 CEST 2020

The build system installs the version of gwascat that is available from git checkout (anticipating that this will propagate). gwascat installs, but fails to pass check -- it is likely broken


in a way that causes your package to fail


On 6/5/20, 6:27 AM, "Bioc-devel on behalf of Robert Castelo" <bioc-devel-bounces using r-project.org on behalf of robert.castelo using upf.edu> wrote:


    my package GenomicScores is not building, see:


    apparently, it is breaking in the following lines of its vignette:


    which in the report from the bioc build machine says:

    gwascat loaded.  Use makeCurrentGwascat() to extract current image.
      from EBI.  The data folder of this package has some legacy extracts.
    Quitting from lines 404-408 (GenomicScores.Rmd)
    Error: processing vignette 'GenomicScores.Rmd' failed with diagnostics:
    object 'ebicat37' not found
    --- failed re-building ‘GenomicScores.Rmd’

    however, in my installation of current bioc-devel on R-4.0 with all 
    packages up to date, GenomicScores builds fine and i cannot reproduce 
    this error. below you can find my session information after the previous 
    two instructions. the logs of 'gwascat' show changes in May 2nd that 
    could be potentially responsible for this but the fact is that 'gwascat' 
    is not building either and it does not seem that the changes propagate 
    through the build system, its version is still 2.21.0, on which 
    GenomicScores built without problems for the current release.

    i'm cc'ing this email to Vince, as maintainer of 'gwascat', in case he 
    has some more specific suggestion about this but any hint will be 
    greatly appreciated.


    R version 4.0.0 (2020-04-24)
    Platform: x86_64-pc-linux-gnu (64-bit)
    Running under: CentOS Linux 7 (Core)

    Matrix products: default
    BLAS:   /opt/R/R-4.0.0/lib64/R/lib/libRblas.so
    LAPACK: /opt/R/R-4.0.0/lib64/R/lib/libRlapack.so

      [1] LC_CTYPE=en_US.UTF8       LC_NUMERIC=C
      [3] LC_TIME=en_US.UTF8        LC_COLLATE=en_US.UTF8
      [7] LC_PAPER=en_US.UTF8       LC_NAME=C
      [9] LC_ADDRESS=C              LC_TELEPHONE=C

    attached base packages:
    [1] stats     graphics  grDevices utils     datasets methods   base

    other attached packages:
    [1] gwascat_2.21.0 colorout_1.2-2

    loaded via a namespace (and not attached):
      [1] Rcpp_1.0.4.6 lattice_0.20-41
      [3] prettyunits_1.1.1 Rsamtools_2.5.1
      [5] Biostrings_2.57.1 assertthat_0.2.1
      [7] digest_0.6.25 BiocFileCache_1.13.0
      [9] R6_2.4.1 GenomeInfoDb_1.25.1
    [11] stats4_4.0.0 RSQLite_2.2.0
    [13] httr_1.4.1 ggplot2_3.3.1
    [15] pillar_1.4.4 zlibbioc_1.35.0
    [17] rlang_0.4.6 GenomicFeatures_1.41.0
    [19] progress_1.2.2 curl_4.3
    [21] blob_1.2.1 S4Vectors_0.27.11
    [23] Matrix_1.2-18 BiocParallel_1.23.0
    [25] stringr_1.4.0 RCurl_1.98-1.2
    [27] bit_1.1-15.2 biomaRt_2.45.0
    [29] munsell_0.5.0 DelayedArray_0.15.1
    [31] compiler_4.0.0 rtracklayer_1.49.3
    [33] pkgconfig_2.0.3 askpass_1.1
    [35] BiocGenerics_0.35.3 openssl_1.4.1
    [37] tidyselect_1.1.0 SummarizedExperiment_1.19.4
    [39] tibble_3.0.1 GenomeInfoDbData_1.2.3
    [41] IRanges_2.23.7 matrixStats_0.56.0
    [43] XML_3.99-0.3 crayon_1.3.4
    [45] dplyr_1.0.0 dbplyr_1.4.4
    [47] GenomicAlignments_1.25.1 bitops_1.0-6
    [49] rappdirs_0.3.1 grid_4.0.0
    [51] gtable_0.3.0 lifecycle_0.2.0
    [53] DBI_1.1.0 magrittr_1.5
    [55] scales_1.1.1 stringi_1.4.6
    [57] XVector_0.29.1 ellipsis_0.3.1
    [59] generics_0.0.2 vctrs_0.3.0
    [61] tools_4.0.0 bit64_0.9-7
    [63] Biobase_2.49.0 glue_1.4.1
    [65] purrr_0.3.4 hms_0.5.3
    [67] parallel_4.0.0 colorspace_1.4-1
    [69] AnnotationDbi_1.51.0 GenomicRanges_1.41.3
    [71] memoise_1.1.0

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