[Bioc-devel] gwaswloc class broken

[Robert Castelo]

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