hi,
the 'gwasloc' class from the gwascat package seems to be broken in
devel, i suspect due to recent changes in the 'GRanges' class or some
other class upstream, because the definition of the 'gwasloc' class in
gwascat/R/classes.R is:
setClass("gwaswloc", representation(extractDate="character"),
contains="GRanges")
i paste below a minimal example, traceback and (very long) corresponding
session info. i'm using it in the vignette of GenomicScores, so it's not
so crucial but it would be nice to have it working again. thanks!!
library(gwascat)
data(ebicat37)
class(ebicat37)
[1] "gwaswloc"
attr(,"package")
[1] "gwascat"
ebicat37[1]
Error in updateObject(x, check = FALSE) :
no slot of name "elementType" for this object of class "gwaswloc"
9: updateObject(x, check = FALSE)
8: updateObject(x, check = FALSE)
7: extractROWS(x, i)
6: extractROWS(x, i)
5: subset_along_ROWS(x, i, , ..., drop = drop)
4: .nextMethod(x = x, i = i)
3: callNextMethod()
2: ebicat37[1]
1: ebicat37[1]
sessionInfo()
R Under development (unstable) (2017-10-30 r73642)
Platform: x86_64-pc-linux-gnu (64-bit)
Running under: CentOS Linux 7 (Core)
Matrix products: default
BLAS: /opt/R/R-devel/lib64/R/lib/libRblas.so
LAPACK: /opt/R/R-devel/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] parallel stats4 stats graphics grDevices utils datasets
[8] methods base
other attached packages:
[1] gwascat_2.11.1
[2] Homo.sapiens_1.3.1
[3] TxDb.Hsapiens.UCSC.hg19.knownGene_3.2.2
[4] org.Hs.eg.db_3.5.0
[5] GO.db_3.5.0
[6] OrganismDbi_1.21.1
[7] GenomicFeatures_1.31.10
[8] GenomicRanges_1.31.22
[9] GenomeInfoDb_1.15.5
[10] AnnotationDbi_1.41.4
[11] IRanges_2.13.26
[12] S4Vectors_0.17.33
[13] Biobase_2.39.2
[14] BiocGenerics_0.25.3
[15] colorout_1.1-3
loaded via a namespace (and not attached):
[1] ggbeeswarm_0.6.0 colorspace_1.3-2
[3] biovizBase_1.27.1 htmlTable_1.11.2
[5] XVector_0.19.8 base64enc_0.1-3
[7] dichromat_2.0-0 rstudioapi_0.7
[9] bit64_0.9-7 interactiveDisplayBase_1.17.0
[11] codetools_0.2-15 splines_3.5.0
[13] snpStats_1.29.1 ggbio_1.27.1
[15] doParallel_1.0.11 knitr_1.19
[17] Formula_1.2-2 jsonlite_1.5
[19] gQTLBase_1.11.0 Rsamtools_1.31.3
[21] cluster_2.0.6 graph_1.57.1
[23] shiny_1.0.5 compiler_3.5.0
[25] httr_1.3.1 backports_1.1.2
[27] assertthat_0.2.0 Matrix_1.2-12
[29] lazyeval_0.2.1 limma_3.35.11
[31] acepack_1.4.1 htmltools_0.3.6
[33] prettyunits_1.0.2 tools_3.5.0
[35] bindrcpp_0.2 gtable_0.2.0
[37] glue_1.2.0 GenomeInfoDbData_1.1.0
[39] reshape2_1.4.3 dplyr_0.7.4
[41] fastmatch_1.1-0 Rcpp_0.12.15
[43] Biostrings_2.47.9 nlme_3.1-135.5
[45] rtracklayer_1.39.9 iterators_1.0.9
[47] ffbase_0.12.3 stringr_1.3.0
[49] mime_0.5 ensembldb_2.3.11
[51] XML_3.98-1.10 AnnotationHub_2.11.2
[53] zlibbioc_1.25.0 scales_0.5.0
[55] BSgenome_1.47.5 VariantAnnotation_1.25.12
[57] BiocInstaller_1.29.4 ProtGenerics_1.11.0
[59] SummarizedExperiment_1.9.14 RBGL_1.55.0
[61] AnnotationFilter_1.3.2 RColorBrewer_1.1-2
[63] BBmisc_1.11 yaml_2.1.16
[65] curl_3.1 memoise_1.1.0
[67] gridExtra_2.3 ggplot2_2.2.1
[69] rpart_4.1-12 biomaRt_2.35.10
[71] latticeExtra_0.6-28 reshape_0.8.7
[73] stringi_1.1.6 RSQLite_2.0
[75] foreach_1.4.4 RMySQL_0.10.13
[77] checkmate_1.8.5 BiocParallel_1.13.1
[79] rlang_0.1.6 pkgconfig_2.0.1
[81] BatchJobs_1.7 GenomicFiles_1.15.2
[83] matrixStats_0.53.1 bitops_1.0-6
[85] lattice_0.20-35 purrr_0.2.4
[87] bindr_0.1 GenomicAlignments_1.15.12
[89] htmlwidgets_1.0 bit_1.1-12
[91] GGally_1.3.2 plyr_1.8.4
[93] magrittr_1.5 sendmailR_1.2-1
[95] R6_2.2.2 Hmisc_4.1-1
[97] erma_0.11.6 DelayedArray_0.5.20
[99] DBI_0.7 foreign_0.8-70
[101] pillar_1.1.0 mgcv_1.8-23
[103] nnet_7.3-12 survival_2.41-3
[105] RCurl_1.95-4.10 tibble_1.4.2
[107] plotly_4.7.1 progress_1.1.2
[109] grid_3.5.0 data.table_1.10.4-3
[111] blob_1.1.0 gQTLstats_1.11.4
[113] digest_0.6.15 xtable_1.8-2
[115] ff_2.2-13 tidyr_0.8.0
[117] httpuv_1.3.5 brew_1.0-6
[119] munsell_0.4.3 beeswarm_0.2.3
[121] viridisLite_0.3.0 Gviz_1.23.3
[123] vipor_0.4.5
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