Computing gene models (unable to find an inherited method for function ‘ranges’ for signature ‘"SortedByQueryHits"’)

[AMChalkie]

Hi,

Thanks for the package. I've just come up against the following error when running goldmine. Thinks were working fine a while ago, so it might be related to changes in another class.

Cheers
/Alistair

trying URL 'http://hgdownload.cse.ucsc.edu/goldenPath/mm10/database/refFlat.txt.gz'
Content type 'application/x-gzip' length 4015306 bytes (3.8 MB)

downloaded 3.8 MB

trying URL 'http://hgdownload.cse.ucsc.edu/goldenPath/mm10/database/refFlat.sql'
Content type 'text/plain; charset=UTF-8' length 1754 bytes

downloaded 1754 bytes

Computing gene models
Generating context annotation - genes
Error in (function (classes, fdef, mtable) :
unable to find an inherited method for function ‘ranges’ for signature ‘"SortedByQueryHits"’
Called from: (function (classes, fdef, mtable)
{
methods <- .findInheritedMethods(classes, fdef, mtable)
if (length(methods) == 1L)
return(methods[[1L]])
else if (length(methods) == 0L) {
cnames <- paste0(""", vapply(classes, as.character,
""), """, collapse = ", ")
stop(gettextf("unable to find an inherited method for function %s for signature %s",
sQuote(fdef@generic), sQuote(cnames)), domain = NA)
}
else stop("Internal error in finding inherited methods; didn't return a unique method",
domain = NA)
})(list("SortedByQueryHits"), new("standardGeneric", .Data = function (x,
use.names = TRUE, use.mcols = FALSE, ...)
standardGeneric("ranges"), generic = "ranges", package = "IRanges",
group = list(), valueClass = character(0), signature = "x",
default = NULL, skeleton = (function (x, use.names = TRUE,
use.mcols = FALSE, ...)
stop("invalid call in method dispatch to 'ranges' (no default method)",
domain = NA))(x, use.names, use.mcols, ...)), )
Browse[1]> dim(data.annotated)
Error during wrapup: object 'data.annotated' not found
Browse[1]>
R.3.5.2.>
R.3.5.2.>traceback()
11: stop(gettextf("unable to find an inherited method for function %s for signature %s",
sQuote(fdef@generic), sQuote(cnames)), domain = NA)
10: (function (classes, fdef, mtable)
{
methods <- .findInheritedMethods(classes, fdef, mtable)
if (length(methods) == 1L)
return(methods[[1L]])
else if (length(methods) == 0L) {
cnames <- paste0(""", vapply(classes, as.character,
""), """, collapse = ", ")
stop(gettextf("unable to find an inherited method for function %s for signature %s",
sQuote(fdef@generic), sQuote(cnames)), domain = NA)
}
else stop("Internal error in finding inherited methods; didn't return a unique method",
domain = NA)
})(list("SortedByQueryHits"), new("standardGeneric", .Data = function (x,
use.names = TRUE, use.mcols = FALSE, ...)
standardGeneric("ranges"), generic = "ranges", package = "IRanges",
group = list(), valueClass = character(0), signature = "x",
default = NULL, skeleton = (function (x, use.names = TRUE,
use.mcols = FALSE, ...)
stop("invalid call in method dispatch to 'ranges' (no default method)",
domain = NA))(x, use.names, use.mcols, ...)), )
9: ranges(overlaps.fo, ranges(query.gr), ranges(subject.gr)) at annotate.r#518
8: goldmine:::calcPercentOverlap(query.gr, reduce(x)) at annotate.r#46
7: FUN(X[[i]], ...)
6: lapply(genemodels, function(x) goldmine:::calcPercentOverlap(query.gr,
reduce(x)))
5: lapply(genemodels, function(x) goldmine:::calcPercentOverlap(query.gr,
reduce(x))) at annotate.r#46
4: withCallingHandlers(expr, warning = function(w) invokeRestart("muffleWarning"))
3: suppressWarnings(lapply(genemodels, function(x) goldmine:::calcPercentOverlap(query.gr,
reduce(x)))) at annotate.r#46
2: goldmine(query = query, genes = getGenes("refseq", genome = genome,
cachedir), genome = genome, cachedir = cachedir) at

R.3.5.2.>sessionInfo()
R version 3.5.2 (2018-12-20)
Platform: x86_64-apple-darwin15.6.0 (64-bit)
Running under: macOS High Sierra 10.13.6

Matrix products: default
BLAS: /System/Library/Frameworks/Accelerate.framework/Versions/A/Frameworks/vecLib.framework/Versions/A/libBLAS.dylib
LAPACK: /Library/Frameworks/R.framework/Versions/3.5/Resources/lib/libRlapack.dylib

locale:
[1] en_AU.UTF-8/en_AU.UTF-8/en_AU.UTF-8/C/en_AU.UTF-8/en_AU.UTF-8

attached base packages:
[1] parallel stats4 stats graphics grDevices utils datasets methods base

other attached packages:
[1] usethis_1.4.0 devtools_2.0.1 goldmine_1.0 ggplot2_3.1.0 stringr_1.3.1 GenomicRanges_1.34.0 GenomeInfoDb_1.18.1 IRanges_2.16.0 S4Vectors_0.20.1 BiocGenerics_0.28.0
[11] data.table_1.11.8

loaded via a namespace (and not attached):
[1] tidyselect_0.2.5 remotes_2.0.2 purrr_0.2.5 testthat_2.0.1 colorspace_1.3-2 yaml_2.2.0 base64enc_0.1-3 rlang_0.3.0.1
[9] pkgbuild_1.0.2 R.oo_1.22.0 pillar_1.3.0 glue_1.3.0 withr_2.1.2 R.utils_2.7.0 sessioninfo_1.1.1 bindrcpp_0.2.2
[17] GenomeInfoDbData_1.2.0 bindr_0.1.1 plyr_1.8.4 zlibbioc_1.28.0 munsell_0.5.0 gtable_0.2.0 R.methodsS3_1.7.1 memoise_1.1.0
[25] callr_3.0.0 ps_1.2.1 curl_3.2 Rcpp_1.0.0 backports_1.1.2 scales_1.0.0 desc_1.2.0 pkgload_1.0.2
[33] XVector_0.22.0 fs_1.2.6 digest_0.6.18 stringi_1.2.4 processx_3.2.1 dplyr_0.7.8 alistairsRfunctions_0.046 grid_3.5.2
[41] rprojroot_1.3-2 cli_1.0.1 tools_3.5.2 bitops_1.0-6 magrittr_1.5 lazyeval_0.2.1 RCurl_1.95-4.11 tibble_1.4.2
[49] crayon_1.3.4 pkgconfig_2.0.2 prettyunits_1.0.2 assertthat_0.2.0 httr_1.3.1 rstudioapi_0.8 R6_2.3.0 compiler_3.5.2

[ghost]

Hi AMChalkie,
Have you found a solution for the error? I've got the same error, too.

Thanks in advance.

[AMChalkie]

Fixed on https://github.com/AMChalkie/goldmine [and subsequently messed up again... still working on it]
(Essentially findOverlaps -> GRanges::findOverlaps)