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

I am really sorry about the situation with gwascat and will try to 
straighten it out today.

On Fri, Jun 5, 2020 at 6:27 AM Robert Castelo <robert.castelo at upf.edu 
<mailto:robert.castelo at upf.edu>> wrote:

    hi,

    my package GenomicScores is not building, see:

    http://bioconductor.org/checkResults/devel/bioc-LATEST/GenomicScores/malbec1-buildsrc.html

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

    library(gwascat)
    data(ebicat37)

    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.

    thanks!!

    sessionInfo()
    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

    locale:
    ?[1] LC_CTYPE=en_US.UTF8 LC_NUMERIC=C
    ?[3] LC_TIME=en_US.UTF8 LC_COLLATE=en_US.UTF8
    ?[5] LC_MONETARY=en_US.UTF8 LC_MESSAGES=en_US.UTF8
    ?[7] LC_PAPER=en_US.UTF8 LC_NAME=C
    ?[9] LC_ADDRESS=C LC_TELEPHONE=C
    [11] LC_MEASUREMENT=en_US.UTF8 LC_IDENTIFICATION=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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