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

[Robert Castelo]

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?

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 using upf.edu 
> <mailto:robert.castelo using 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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