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

On Fri, Jun 5, 2020 at 10:24 AM Robert Castelo <robert.castelo at upf.edu 
<mailto:robert.castelo at upf.edu>> wrote:

    hi Vince,

    no worries, i've been finally able to reproduce the error in my
    computer and i'm afraid i'm probably using a deprecated dataset
    from 'gwascat', concretely the one that was stored as

    gwascat/data/ebicat37.rda

    what would be the replacement for the following kind of operation?


The best thing to do from a scientific point of view would likely be

curcat = gwascat::makeCurrentGwascat()

then work with that, which will have GRCh38 coordinates.

It is slow to run makeCurrentGwascat.? You might want to serialize 
what you need.
I can't place a snapshot in gwascat as I had in the past because the 
image compressed
with xz exceeds 5MB.? Any snapshot has to be in AnnotationHub.? I 
don't have a
plan for this at the moment.

There is an object called ebicat_2020_04_30 in the data
folder of gwascat on devel branch.? It is a sample of 50000 records 
from the full
catalog of that date.? You might be able to use that for what you are 
doing; I will
be renaming it to clarify that it is a sample.


    data(ebicat37)
    eyersids <- unique(subsetByTraits(ebicat37, tr="Eye color")$SNPS)
    eyersids
    ?[1] "rs12913832" "rs7173419"? "rs3002288" "rs12896399" "rs1408799"
    ?[6] "rs12520016" "rs288139"?? "rs1667394" "rs4596632"? "rs12203592"
    [11] "rs16891982" "rs1393350"? "rs1847134"

    thanks!

    robert.

    On 05/06/2020 14:06, Vincent Carey wrote:

    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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