On Fri, Jun 5, 2020 at 10:24 AM Robert Castelo <robert.cast...@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.cast...@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 >> >> >> > The information in this e-mail is intended only for the person to whom it > is > addressed. 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