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>
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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