BioC 3.3: CHECK report for epivizrData on morelia

Package: epivizrData

Version: 0.99.3

Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings epivizrData_0.99.3.tar.gz

StartedAt: 2016-04-21 02:07:05 -0700 (Thu, 21 Apr 2016)

EndedAt: 2016-04-21 02:10:39 -0700 (Thu, 21 Apr 2016)

EllapsedTime: 213.3 seconds

RetCode: 1

Status:  ERROR

CheckDir: epivizrData.Rcheck

Warnings: NA

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###
### Running command:
###
###   /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings epivizrData_0.99.3.tar.gz
###
##############################################################################
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* using log directory ‘/Users/biocbuild/bbs-3.3-bioc/meat/epivizrData.Rcheck’
* using R version 3.3.0 beta (2016-04-06 r70435)
* using platform: x86_64-apple-darwin13.4.0 (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘epivizrData/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘epivizrData’ version ‘0.99.3’
* checking package namespace information ... OK
* checking package dependencies ... OK
* checking if this is a source package ... OK
* checking if there is a namespace ... OK
* checking for hidden files and directories ... OK
* checking for portable file names ... OK
* checking for sufficient/correct file permissions ... OK
* checking whether package ‘epivizrData’ can be installed ... [20s/22s] OK
* checking installed package size ... OK
* checking package directory ... OK
* checking ‘build’ directory ... OK
* checking DESCRIPTION meta-information ... OK
* checking top-level files ... OK
* checking for left-over files ... OK
* checking index information ... OK
* checking package subdirectories ... OK
* checking R files for non-ASCII characters ... OK
* checking R files for syntax errors ... OK
* checking whether the package can be loaded ... OK
* checking whether the package can be loaded with stated dependencies ... OK
* checking whether the package can be unloaded cleanly ... OK
* checking whether the namespace can be loaded with stated dependencies ... OK
* checking whether the namespace can be unloaded cleanly ... OK
* checking dependencies in R code ... OK
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... OK
* checking Rd files ... OK
* checking Rd metadata ... OK
* checking Rd cross-references ... OK
* checking for missing documentation entries ... OK
* checking for code/documentation mismatches ... OK
* checking Rd \usage sections ... OK
* checking Rd contents ... OK
* checking for unstated dependencies in examples ... OK
* checking installed files from ‘inst/doc’ ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... [10s/11s] OK
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
  Running ‘testthat.R’ [21s/22s]
 ERROR
Running the tests in ‘tests/testthat.R’ failed.
Last 13 lines of output:
  1. Error: block data fetch works (@test-data_fetch.R#4) 
  2. Error: block data fetch works (@test-data_fetch.R#4) 
  3. Error: block data fetch works (@test-data_fetch.R#4) 
  4. Error: block data fetch works (@test-data_fetch.R#4) 
  5. Error: block data fetch works (@test-data_fetch.R#4) 
  6. Error: block data fetch works (@test-data_fetch.R#4) 
  7. Error: block data fetch works (@test-data_fetch.R#4) 
  8. Error: block data fetch works (@test-data_fetch.R#4) 
  9. Error: block data fetch works (@test-data_fetch.R#4) 
  1. ...
  
  Error: testthat unit tests failed
  Execution halted
* checking for unstated dependencies in vignettes ... OK
* checking package vignettes in ‘inst/doc’ ... OK
* checking running R code from vignettes ... SKIPPED
* checking re-building of vignette outputs ... SKIPPED
* checking PDF version of manual ... OK
* DONE

Status: 1 ERROR
See
  ‘/Users/biocbuild/bbs-3.3-bioc/meat/epivizrData.Rcheck/00check.log’
for details.

R version 3.3.0 beta (2016-04-06 r70435) -- "Supposedly Educational"
Copyright (C) 2016 The R Foundation for Statistical Computing
Platform: x86_64-apple-darwin13.4.0 (64-bit)

R is free software and comes with ABSOLUTELY NO WARRANTY.
You are welcome to redistribute it under certain conditions.
Type 'license()' or 'licence()' for distribution details.

R is a collaborative project with many contributors.
Type 'contributors()' for more information and
'citation()' on how to cite R or R packages in publications.

Type 'demo()' for some demos, 'help()' for on-line help, or
'help.start()' for an HTML browser interface to help.
Type 'q()' to quit R.

> library(testthat)
> library(epivizrData)
Loading required package: epivizrServer
Loading required package: Biobase
Loading required package: BiocGenerics
Loading required package: parallel

Attaching package: 'BiocGenerics'

The following objects are masked from 'package:parallel':

    clusterApply, clusterApplyLB, clusterCall, clusterEvalQ,
    clusterExport, clusterMap, parApply, parCapply, parLapply,
    parLapplyLB, parRapply, parSapply, parSapplyLB

The following objects are masked from 'package:stats':

    IQR, mad, xtabs

The following objects are masked from 'package:base':

    Filter, Find, Map, Position, Reduce, anyDuplicated, append,
    as.data.frame, cbind, colnames, do.call, duplicated, eval, evalq,
    get, grep, grepl, intersect, is.unsorted, lapply, lengths, mapply,
    match, mget, order, paste, pmax, pmax.int, pmin, pmin.int, rank,
    rbind, rownames, sapply, setdiff, sort, table, tapply, union,
    unique, unsplit

Welcome to Bioconductor

    Vignettes contain introductory material; view with
    'browseVignettes()'. To cite Bioconductor, see
    'citation("Biobase")', and for packages 'citation("pkgname")'.

> 
> test_check("epivizrData")
1. Error: block data fetch works (@test-data_fetch.R#4) ------------------------
attempt to apply non-function
1: GRanges(seqnames = "chr1", ranges = IRanges::IRanges(start = 1:10, width = 1), seqinfo = Seqinfo(seqnames = "chr1", 
       genome = "hcb")) at testthat/test-data_fetch.R:4
2: newGRanges("GRanges", seqnames = seqnames, ranges = ranges, strand = strand, mcols = DataFrame(..., 
       check.names = FALSE), seqlengths = seqlengths, seqinfo = seqinfo)
3: `runValue<-`(`*tmp*`, value = structure(1L, .Label = "chr1", class = "factor"))
4: `runValue<-`(`*tmp*`, value = structure(1L, .Label = "chr1", class = "factor"))
5: Rle(value, runLength(x))
6: (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("factor"), structure(function (values = logical(0), lengths = integer(0)) 
   standardGeneric("Rle"), generic = structure("Rle", package = "S4Vectors"), package = "S4Vectors", group = list(), valueClass = character(0), signature = "values", default = `\001NULL\001`, skeleton = (function (values = logical(0), 
       lengths = integer(0)) 
   stop("invalid call in method dispatch to 'Rle' (no default method)", domain = NA))(values, 
       lengths), class = structure("standardGeneric", package = "methods")), <environment>)
7: .findInheritedMethods(classes, fdef, mtable)
8: .newSignature(classes, fdef@signature)
9: .asS4(structure(as.character(classes)[i], class = .signatureClassName, names = as.character(names)[i], 
       package = pkgs))
10: asS4(object, TRUE, 0L)
11: structure(as.character(classes)[i], class = .signatureClassName, names = as.character(names)[i], 
       package = pkgs)
12: match(names(attrib), specials)
13: (function (x) 
   x$.self$finalize())(<environment>)

Error in signalCondition(e) : 
  no function to return from, jumping to top level
Calls: <Anonymous> -> .handleSimpleError -> h -> signalCondition
2. Error: block data fetch works (@test-data_fetch.R#4) ------------------------
attempt to apply non-function
1: GRanges(seqnames = "chr1", ranges = IRanges::IRanges(start = 1:10, width = 1), seqinfo = Seqinfo(seqnames = "chr1", 
       genome = "hcb")) at testthat/test-data_fetch.R:4
2: newGRanges("GRanges", seqnames = seqnames, ranges = ranges, strand = strand, mcols = DataFrame(..., 
       check.names = FALSE), seqlengths = seqlengths, seqinfo = seqinfo)
3: `runValue<-`(`*tmp*`, value = structure(1L, .Label = "chr1", class = "factor"))
4: `runValue<-`(`*tmp*`, value = structure(1L, .Label = "chr1", class = "factor"))
5: Rle(value, runLength(x))
6: (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("factor"), structure(function (values = logical(0), lengths = integer(0)) 
   standardGeneric("Rle"), generic = structure("Rle", package = "S4Vectors"), package = "S4Vectors", group = list(), valueClass = character(0), signature = "values", default = `\001NULL\001`, skeleton = (function (values = logical(0), 
       lengths = integer(0)) 
   stop("invalid call in method dispatch to 'Rle' (no default method)", domain = NA))(values, 
       lengths), class = structure("standardGeneric", package = "methods")), <environment>)
7: .findInheritedMethods(classes, fdef, mtable)
8: .newSignature(classes, fdef@signature)
9: .asS4(structure(as.character(classes)[i], class = .signatureClassName, names = as.character(names)[i], 
       package = pkgs))
10: asS4(object, TRUE, 0L)
11: structure(as.character(classes)[i], class = .signatureClassName, names = as.character(names)[i], 
       package = pkgs)
12: match(names(attrib), specials)
13: (function (x) 
   x$.self$finalize())(<environment>)

Error in signalCondition(e) : 
  no function to return from, jumping to top level
Calls: <Anonymous> -> .handleSimpleError -> h -> signalCondition
3. Error: block data fetch works (@test-data_fetch.R#4) ------------------------
attempt to apply non-function
1: GRanges(seqnames = "chr1", ranges = IRanges::IRanges(start = 1:10, width = 1), seqinfo = Seqinfo(seqnames = "chr1", 
       genome = "hcb")) at testthat/test-data_fetch.R:4
2: newGRanges("GRanges", seqnames = seqnames, ranges = ranges, strand = strand, mcols = DataFrame(..., 
       check.names = FALSE), seqlengths = seqlengths, seqinfo = seqinfo)
3: `runValue<-`(`*tmp*`, value = structure(1L, .Label = "chr1", class = "factor"))
4: `runValue<-`(`*tmp*`, value = structure(1L, .Label = "chr1", class = "factor"))
5: Rle(value, runLength(x))
6: (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("factor"), structure(function (values = logical(0), lengths = integer(0)) 
   standardGeneric("Rle"), generic = structure("Rle", package = "S4Vectors"), package = "S4Vectors", group = list(), valueClass = character(0), signature = "values", default = `\001NULL\001`, skeleton = (function (values = logical(0), 
       lengths = integer(0)) 
   stop("invalid call in method dispatch to 'Rle' (no default method)", domain = NA))(values, 
       lengths), class = structure("standardGeneric", package = "methods")), <environment>)
7: .findInheritedMethods(classes, fdef, mtable)
8: .newSignature(classes, fdef@signature)
9: .asS4(structure(as.character(classes)[i], class = .signatureClassName, names = as.character(names)[i], 
       package = pkgs))
10: asS4(object, TRUE, 0L)
11: structure(as.character(classes)[i], class = .signatureClassName, names = as.character(names)[i], 
       package = pkgs)
12: match(names(attrib), specials)
13: (function (x) 
   x$.self$finalize())(<environment>)

Error in signalCondition(e) : 
  no function to return from, jumping to top level
Calls: <Anonymous> -> .handleSimpleError -> h -> signalCondition
4. Error: block data fetch works (@test-data_fetch.R#4) ------------------------
attempt to apply non-function
1: GRanges(seqnames = "chr1", ranges = IRanges::IRanges(start = 1:10, width = 1), seqinfo = Seqinfo(seqnames = "chr1", 
       genome = "hcb")) at testthat/test-data_fetch.R:4
2: newGRanges("GRanges", seqnames = seqnames, ranges = ranges, strand = strand, mcols = DataFrame(..., 
       check.names = FALSE), seqlengths = seqlengths, seqinfo = seqinfo)
3: `runValue<-`(`*tmp*`, value = structure(1L, .Label = "chr1", class = "factor"))
4: `runValue<-`(`*tmp*`, value = structure(1L, .Label = "chr1", class = "factor"))
5: Rle(value, runLength(x))
6: (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("factor"), structure(function (values = logical(0), lengths = integer(0)) 
   standardGeneric("Rle"), generic = structure("Rle", package = "S4Vectors"), package = "S4Vectors", group = list(), valueClass = character(0), signature = "values", default = `\001NULL\001`, skeleton = (function (values = logical(0), 
       lengths = integer(0)) 
   stop("invalid call in method dispatch to 'Rle' (no default method)", domain = NA))(values, 
       lengths), class = structure("standardGeneric", package = "methods")), <environment>)
7: .findInheritedMethods(classes, fdef, mtable)
8: .newSignature(classes, fdef@signature)
9: .asS4(structure(as.character(classes)[i], class = .signatureClassName, names = as.character(names)[i], 
       package = pkgs))
10: asS4(object, TRUE, 0L)
11: structure(as.character(classes)[i], class = .signatureClassName, names = as.character(names)[i], 
       package = pkgs)
12: match(names(attrib), specials)
13: (function (x) 
   x$.self$finalize())(<environment>)

Error in signalCondition(e) : 
  no function to return from, jumping to top level
Calls: <Anonymous> -> .handleSimpleError -> h -> signalCondition
5. Error: block data fetch works (@test-data_fetch.R#4) ------------------------
attempt to apply non-function
1: GRanges(seqnames = "chr1", ranges = IRanges::IRanges(start = 1:10, width = 1), seqinfo = Seqinfo(seqnames = "chr1", 
       genome = "hcb")) at testthat/test-data_fetch.R:4
2: newGRanges("GRanges", seqnames = seqnames, ranges = ranges, strand = strand, mcols = DataFrame(..., 
       check.names = FALSE), seqlengths = seqlengths, seqinfo = seqinfo)
3: `runValue<-`(`*tmp*`, value = structure(1L, .Label = "chr1", class = "factor"))
4: `runValue<-`(`*tmp*`, value = structure(1L, .Label = "chr1", class = "factor"))
5: Rle(value, runLength(x))
6: (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("factor"), structure(function (values = logical(0), lengths = integer(0)) 
   standardGeneric("Rle"), generic = structure("Rle", package = "S4Vectors"), package = "S4Vectors", group = list(), valueClass = character(0), signature = "values", default = `\001NULL\001`, skeleton = (function (values = logical(0), 
       lengths = integer(0)) 
   stop("invalid call in method dispatch to 'Rle' (no default method)", domain = NA))(values, 
       lengths), class = structure("standardGeneric", package = "methods")), <environment>)
7: .findInheritedMethods(classes, fdef, mtable)
8: .newSignature(classes, fdef@signature)
9: .asS4(structure(as.character(classes)[i], class = .signatureClassName, names = as.character(names)[i], 
       package = pkgs))
10: asS4(object, TRUE, 0L)
11: structure(as.character(classes)[i], class = .signatureClassName, names = as.character(names)[i], 
       package = pkgs)
12: match(names(attrib), specials)
13: (function (x) 
   x$.self$finalize())(<environment>)

Error in signalCondition(e) : 
  no function to return from, jumping to top level
Calls: <Anonymous> -> .handleSimpleError -> h -> signalCondition
6. Error: block data fetch works (@test-data_fetch.R#4) ------------------------
attempt to apply non-function
1: GRanges(seqnames = "chr1", ranges = IRanges::IRanges(start = 1:10, width = 1), seqinfo = Seqinfo(seqnames = "chr1", 
       genome = "hcb")) at testthat/test-data_fetch.R:4
2: newGRanges("GRanges", seqnames = seqnames, ranges = ranges, strand = strand, mcols = DataFrame(..., 
       check.names = FALSE), seqlengths = seqlengths, seqinfo = seqinfo)
3: `runValue<-`(`*tmp*`, value = structure(1L, .Label = "chr1", class = "factor"))
4: `runValue<-`(`*tmp*`, value = structure(1L, .Label = "chr1", class = "factor"))
5: Rle(value, runLength(x))
6: (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("factor"), structure(function (values = logical(0), lengths = integer(0)) 
   standardGeneric("Rle"), generic = structure("Rle", package = "S4Vectors"), package = "S4Vectors", group = list(), valueClass = character(0), signature = "values", default = `\001NULL\001`, skeleton = (function (values = logical(0), 
       lengths = integer(0)) 
   stop("invalid call in method dispatch to 'Rle' (no default method)", domain = NA))(values, 
       lengths), class = structure("standardGeneric", package = "methods")), <environment>)
7: .findInheritedMethods(classes, fdef, mtable)
8: .newSignature(classes, fdef@signature)
9: .asS4(structure(as.character(classes)[i], class = .signatureClassName, names = as.character(names)[i], 
       package = pkgs))
10: asS4(object, TRUE, 0L)
11: structure(as.character(classes)[i], class = .signatureClassName, names = as.character(names)[i], 
       package = pkgs)
12: match(names(attrib), specials)
13: (function (x) 
   x$.self$finalize())(<environment>)

Error in signalCondition(e) : 
  no function to return from, jumping to top level
Calls: <Anonymous> -> .handleSimpleError -> h -> signalCondition
7. Error: block data fetch works (@test-data_fetch.R#4) ------------------------
attempt to apply non-function
1: GRanges(seqnames = "chr1", ranges = IRanges::IRanges(start = 1:10, width = 1), seqinfo = Seqinfo(seqnames = "chr1", 
       genome = "hcb")) at testthat/test-data_fetch.R:4
2: newGRanges("GRanges", seqnames = seqnames, ranges = ranges, strand = strand, mcols = DataFrame(..., 
       check.names = FALSE), seqlengths = seqlengths, seqinfo = seqinfo)
3: `runValue<-`(`*tmp*`, value = structure(1L, .Label = "chr1", class = "factor"))
4: `runValue<-`(`*tmp*`, value = structure(1L, .Label = "chr1", class = "factor"))
5: Rle(value, runLength(x))
6: (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("factor"), structure(function (values = logical(0), lengths = integer(0)) 
   standardGeneric("Rle"), generic = structure("Rle", package = "S4Vectors"), package = "S4Vectors", group = list(), valueClass = character(0), signature = "values", default = `\001NULL\001`, skeleton = (function (values = logical(0), 
       lengths = integer(0)) 
   stop("invalid call in method dispatch to 'Rle' (no default method)", domain = NA))(values, 
       lengths), class = structure("standardGeneric", package = "methods")), <environment>)
7: .findInheritedMethods(classes, fdef, mtable)
8: .newSignature(classes, fdef@signature)
9: .asS4(structure(as.character(classes)[i], class = .signatureClassName, names = as.character(names)[i], 
       package = pkgs))
10: asS4(object, TRUE, 0L)
11: structure(as.character(classes)[i], class = .signatureClassName, names = as.character(names)[i], 
       package = pkgs)
12: match(names(attrib), specials)
13: (function (x) 
   x$.self$finalize())(<environment>)

Error in signalCondition(e) : 
  no function to return from, jumping to top level
Calls: <Anonymous> -> .handleSimpleError -> h -> signalCondition
8. Error: block data fetch works (@test-data_fetch.R#4) ------------------------
attempt to apply non-function
1: GRanges(seqnames = "chr1", ranges = IRanges::IRanges(start = 1:10, width = 1), seqinfo = Seqinfo(seqnames = "chr1", 
       genome = "hcb")) at testthat/test-data_fetch.R:4
2: newGRanges("GRanges", seqnames = seqnames, ranges = ranges, strand = strand, mcols = DataFrame(..., 
       check.names = FALSE), seqlengths = seqlengths, seqinfo = seqinfo)
3: `runValue<-`(`*tmp*`, value = structure(1L, .Label = "chr1", class = "factor"))
4: `runValue<-`(`*tmp*`, value = structure(1L, .Label = "chr1", class = "factor"))
5: Rle(value, runLength(x))
6: (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("factor"), structure(function (values = logical(0), lengths = integer(0)) 
   standardGeneric("Rle"), generic = structure("Rle", package = "S4Vectors"), package = "S4Vectors", group = list(), valueClass = character(0), signature = "values", default = `\001NULL\001`, skeleton = (function (values = logical(0), 
       lengths = integer(0)) 
   stop("invalid call in method dispatch to 'Rle' (no default method)", domain = NA))(values, 
       lengths), class = structure("standardGeneric", package = "methods")), <environment>)
7: .findInheritedMethods(classes, fdef, mtable)
8: .newSignature(classes, fdef@signature)
9: .asS4(structure(as.character(classes)[i], class = .signatureClassName, names = as.character(names)[i], 
       package = pkgs))
10: asS4(object, TRUE, 0L)
11: structure(as.character(classes)[i], class = .signatureClassName, names = as.character(names)[i], 
       package = pkgs)
12: match(names(attrib), specials)
13: (function (x) 
   x$.self$finalize())(<environment>)

Error in signalCondition(e) : 
  no function to return from, jumping to top level
Calls: <Anonymous> -> .handleSimpleError -> h -> signalCondition
9. Error: block data fetch works (@test-data_fetch.R#4) ------------------------
attempt to apply non-function
1: GRanges(seqnames = "chr1", ranges = IRanges::IRanges(start = 1:10, width = 1), seqinfo = Seqinfo(seqnames = "chr1", 
       genome = "hcb")) at testthat/test-data_fetch.R:4
2: newGRanges("GRanges", seqnames = seqnames, ranges = ranges, strand = strand, mcols = DataFrame(..., 
       check.names = FALSE), seqlengths = seqlengths, seqinfo = seqinfo)
3: `runValue<-`(`*tmp*`, value = structure(1L, .Label = "chr1", class = "factor"))
4: `runValue<-`(`*tmp*`, value = structure(1L, .Label = "chr1", class = "factor"))
5: Rle(value, runLength(x))
6: (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("factor"), structure(function (values = logical(0), lengths = integer(0)) 
   standardGeneric("Rle"), generic = structure("Rle", package = "S4Vectors"), package = "S4Vectors", group = list(), valueClass = character(0), signature = "values", default = `\001NULL\001`, skeleton = (function (values = logical(0), 
       lengths = integer(0)) 
   stop("invalid call in method dispatch to 'Rle' (no default method)", domain = NA))(values, 
       lengths), class = structure("standardGeneric", package = "methods")), <environment>)
7: .findInheritedMethods(classes, fdef, mtable)
8: .newSignature(classes, fdef@signature)
9: .asS4(structure(as.character(classes)[i], class = .signatureClassName, names = as.character(names)[i], 
       package = pkgs))
10: asS4(object, TRUE, 0L)
11: structure(as.character(classes)[i], class = .signatureClassName, names = as.character(names)[i], 
       package = pkgs)
12: match(names(attrib), specials)
13: (function (x) 
   x$.self$finalize())(<environment>)

Error in signalCondition(e) : 
  no function to return from, jumping to top level
Calls: <Anonymous> -> .handleSimpleError -> h -> signalCondition
10. Error: block data fetch works (@test-data_fetch.R#4) -----------------------
attempt to apply non-function
1: GRanges(seqnames = "chr1", ranges = IRanges::IRanges(start = 1:10, width = 1), seqinfo = Seqinfo(seqnames = "chr1", 
       genome = "hcb")) at testthat/test-data_fetch.R:4
2: newGRanges("GRanges", seqnames = seqnames, ranges = ranges, strand = strand, mcols = DataFrame(..., 
       check.names = FALSE), seqlengths = seqlengths, seqinfo = seqinfo)
3: `runValue<-`(`*tmp*`, value = structure(1L, .Label = "chr1", class = "factor"))
4: `runValue<-`(`*tmp*`, value = structure(1L, .Label = "chr1", class = "factor"))
5: Rle(value, runLength(x))
6: (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("factor"), structure(function (values = logical(0), lengths = integer(0)) 
   standardGeneric("Rle"), generic = structure("Rle", package = "S4Vectors"), package = "S4Vectors", group = list(), valueClass = character(0), signature = "values", default = `\001NULL\001`, skeleton = (function (values = logical(0), 
       lengths = integer(0)) 
   stop("invalid call in method dispatch to 'Rle' (no default method)", domain = NA))(values, 
       lengths), class = structure("standardGeneric", package = "methods")), <environment>)
7: .findInheritedMethods(classes, fdef, mtable)
8: .newSignature(classes, fdef@signature)
9: .asS4(structure(as.character(classes)[i], class = .signatureClassName, names = as.character(names)[i], 
       package = pkgs))
10: asS4(object, TRUE, 0L)
11: structure(as.character(classes)[i], class = .signatureClassName, names = as.character(names)[i], 
       package = pkgs)
12: match(names(attrib), specials)
13: (function (x) 
   x$.self$finalize())(<environment>)

Error in signalCondition(e) : 
  no function to return from, jumping to top level
Calls: <Anonymous> -> .handleSimpleError -> h -> signalCondition
11. Error: block data fetch works (@test-data_fetch.R#4) -----------------------
attempt to apply non-function
1: GRanges(seqnames = "chr1", ranges = IRanges::IRanges(start = 1:10, width = 1), seqinfo = Seqinfo(seqnames = "chr1", 
       genome = "hcb")) at testthat/test-data_fetch.R:4
2: newGRanges("GRanges", seqnames = seqnames, ranges = ranges, strand = strand, mcols = DataFrame(..., 
       check.names = FALSE), seqlengths = seqlengths, seqinfo = seqinfo)
3: `runValue<-`(`*tmp*`, value = structure(1L, .Label = "chr1", class = "factor"))
4: `runValue<-`(`*tmp*`, value = structure(1L, .Label = "chr1", class = "factor"))
5: Rle(value, runLength(x))
6: (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("factor"), structure(function (values = logical(0), lengths = integer(0)) 
   standardGeneric("Rle"), generic = structure("Rle", package = "S4Vectors"), package = "S4Vectors", group = list(), valueClass = character(0), signature = "values", default = `\001NULL\001`, skeleton = (function (values = logical(0), 
       lengths = integer(0)) 
   stop("invalid call in method dispatch to 'Rle' (no default method)", domain = NA))(values, 
       lengths), class = structure("standardGeneric", package = "methods")), <environment>)
7: .findInheritedMethods(classes, fdef, mtable)
8: .newSignature(classes, fdef@signature)
9: .asS4(structure(as.character(classes)[i], class = .signatureClassName, names = as.character(names)[i], 
       package = pkgs))
10: asS4(object, TRUE, 0L)
11: structure(as.character(classes)[i], class = .signatureClassName, names = as.character(names)[i], 
       package = pkgs)
12: match(names(attrib), specials)
13: (function (x) 
   x$.self$finalize())(<environment>)

Error in signalCondition(e) : 
  no function to return from, jumping to top level
Calls: <Anonymous> -> .handleSimpleError -> h -> signalCondition
12. Error: block data fetch works (@test-data_fetch.R#4) -----------------------
attempt to apply non-function
1: GRanges(seqnames = "chr1", ranges = IRanges::IRanges(start = 1:10, width = 1), seqinfo = Seqinfo(seqnames = "chr1", 
       genome = "hcb")) at testthat/test-data_fetch.R:4
2: newGRanges("GRanges", seqnames = seqnames, ranges = ranges, strand = strand, mcols = DataFrame(..., 
       check.names = FALSE), seqlengths = seqlengths, seqinfo = seqinfo)
3: `runValue<-`(`*tmp*`, value = structure(1L, .Label = "chr1", class = "factor"))
4: `runValue<-`(`*tmp*`, value = structure(1L, .Label = "chr1", class = "factor"))
5: Rle(value, runLength(x))
6: (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("factor"), structure(function (values = logical(0), lengths = integer(0)) 
   standardGeneric("Rle"), generic = structure("Rle", package = "S4Vectors"), package = "S4Vectors", group = list(), valueClass = character(0), signature = "values", default = `\001NULL\001`, skeleton = (function (values = logical(0), 
       lengths = integer(0)) 
   stop("invalid call in method dispatch to 'Rle' (no default method)", domain = NA))(values, 
       lengths), class = structure("standardGeneric", package = "methods")), <environment>)
7: .findInheritedMethods(classes, fdef, mtable)
8: .newSignature(classes, fdef@signature)
9: .asS4(structure(as.character(classes)[i], class = .signatureClassName, names = as.character(names)[i], 
       package = pkgs))
10: asS4(object, TRUE, 0L)
11: structure(as.character(classes)[i], class = .signatureClassName, names = as.character(names)[i], 
       package = pkgs)
12: match(names(attrib), specials)
13: (function (x) 
   x$.self$finalize())(<environment>)

Error in signalCondition(e) : 
  no function to return from, jumping to top level
Calls: <Anonymous> -> .handleSimpleError -> h -> signalCondition
13. Error: block data fetch works (@test-data_fetch.R#4) -----------------------
attempt to apply non-function
1: GRanges(seqnames = "chr1", ranges = IRanges::IRanges(start = 1:10, width = 1), seqinfo = Seqinfo(seqnames = "chr1", 
       genome = "hcb")) at testthat/test-data_fetch.R:4
2: newGRanges("GRanges", seqnames = seqnames, ranges = ranges, strand = strand, mcols = DataFrame(..., 
       check.names = FALSE), seqlengths = seqlengths, seqinfo = seqinfo)
3: `runValue<-`(`*tmp*`, value = structure(1L, .Label = "chr1", class = "factor"))
4: `runValue<-`(`*tmp*`, value = structure(1L, .Label = "chr1", class = "factor"))
5: Rle(value, runLength(x))
6: (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("factor"), structure(function (values = logical(0), lengths = integer(0)) 
   standardGeneric("Rle"), generic = structure("Rle", package = "S4Vectors"), package = "S4Vectors", group = list(), valueClass = character(0), signature = "values", default = `\001NULL\001`, skeleton = (function (values = logical(0), 
       lengths = integer(0)) 
   stop("invalid call in method dispatch to 'Rle' (no default method)", domain = NA))(values, 
       lengths), class = structure("standardGeneric", package = "methods")), <environment>)
7: .findInheritedMethods(classes, fdef, mtable)
8: .newSignature(classes, fdef@signature)
9: .asS4(structure(as.character(classes)[i], class = .signatureClassName, names = as.character(names)[i], 
       package = pkgs))
10: asS4(object, TRUE, 0L)
11: structure(as.character(classes)[i], class = .signatureClassName, names = as.character(names)[i], 
       package = pkgs)
12: match(names(attrib), specials)
13: (function (x) 
   x$.self$finalize())(<environment>)

Error in signalCondition(e) : 
  no function to return from, jumping to top level
Calls: <Anonymous> -> .handleSimpleError -> h -> signalCondition
14. Error: block data fetch works (@test-data_fetch.R#4) -----------------------
attempt to apply non-function
1: GRanges(seqnames = "chr1", ranges = IRanges::IRanges(start = 1:10, width = 1), seqinfo = Seqinfo(seqnames = "chr1", 
       genome = "hcb")) at testthat/test-data_fetch.R:4
2: newGRanges("GRanges", seqnames = seqnames, ranges = ranges, strand = strand, mcols = DataFrame(..., 
       check.names = FALSE), seqlengths = seqlengths, seqinfo = seqinfo)
3: `runValue<-`(`*tmp*`, value = structure(1L, .Label = "chr1", class = "factor"))
4: `runValue<-`(`*tmp*`, value = structure(1L, .Label = "chr1", class = "factor"))
5: Rle(value, runLength(x))
6: (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("factor"), structure(function (values = logical(0), lengths = integer(0)) 
   standardGeneric("Rle"), generic = structure("Rle", package = "S4Vectors"), package = "S4Vectors", group = list(), valueClass = character(0), signature = "values", default = `\001NULL\001`, skeleton = (function (values = logical(0), 
       lengths = integer(0)) 
   stop("invalid call in method dispatch to 'Rle' (no default method)", domain = NA))(values, 
       lengths), class = structure("standardGeneric", package = "methods")), <environment>)
7: .findInheritedMethods(classes, fdef, mtable)
8: .newSignature(classes, fdef@signature)
9: .asS4(structure(as.character(classes)[i], class = .signatureClassName, names = as.character(names)[i], 
       package = pkgs))
10: asS4(object, TRUE, 0L)
11: structure(as.character(classes)[i], class = .signatureClassName, names = as.character(names)[i], 
       package = pkgs)
12: match(names(attrib), specials)
13: (function (x) 
   x$.self$finalize())(<environment>)

Error in signalCondition(e) : 
  no function to return from, jumping to top level
Calls: <Anonymous> -> .handleSimpleError -> h -> signalCondition
15. Error: block data fetch works (@test-data_fetch.R#4) -----------------------
attempt to apply non-function
1: GRanges(seqnames = "chr1", ranges = IRanges::IRanges(start = 1:10, width = 1), seqinfo = Seqinfo(seqnames = "chr1", 
       genome = "hcb")) at testthat/test-data_fetch.R:4
2: newGRanges("GRanges", seqnames = seqnames, ranges = ranges, strand = strand, mcols = DataFrame(..., 
       check.names = FALSE), seqlengths = seqlengths, seqinfo = seqinfo)
3: `runValue<-`(`*tmp*`, value = structure(1L, .Label = "chr1", class = "factor"))
4: `runValue<-`(`*tmp*`, value = structure(1L, .Label = "chr1", class = "factor"))
5: Rle(value, runLength(x))
6: (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("factor"), structure(function (values = logical(0), lengths = integer(0)) 
   standardGeneric("Rle"), generic = structure("Rle", package = "S4Vectors"), package = "S4Vectors", group = list(), valueClass = character(0), signature = "values", default = `\001NULL\001`, skeleton = (function (values = logical(0), 
       lengths = integer(0)) 
   stop("invalid call in method dispatch to 'Rle' (no default method)", domain = NA))(values, 
       lengths), class = structure("standardGeneric", package = "methods")), <environment>)
7: .findInheritedMethods(classes, fdef, mtable)
8: .newSignature(classes, fdef@signature)
9: .asS4(structure(as.character(classes)[i], class = .signatureClassName, names = as.character(names)[i], 
       package = pkgs))
10: asS4(object, TRUE, 0L)
11: structure(as.character(classes)[i], class = .signatureClassName, names = as.character(names)[i], 
       package = pkgs)
12: match(names(attrib), specials)
13: (function (x) 
   x$.self$finalize())(<environment>)

Error in signalCondition(e) : 
  no function to return from, jumping to top level
Calls: <Anonymous> -> .handleSimpleError -> h -> signalCondition
16. Error: block data fetch works (@test-data_fetch.R#4) -----------------------
attempt to apply non-function
1: GRanges(seqnames = "chr1", ranges = IRanges::IRanges(start = 1:10, width = 1), seqinfo = Seqinfo(seqnames = "chr1", 
       genome = "hcb")) at testthat/test-data_fetch.R:4
2: newGRanges("GRanges", seqnames = seqnames, ranges = ranges, strand = strand, mcols = DataFrame(..., 
       check.names = FALSE), seqlengths = seqlengths, seqinfo = seqinfo)
3: `runValue<-`(`*tmp*`, value = structure(1L, .Label = "chr1", class = "factor"))
4: `runValue<-`(`*tmp*`, value = structure(1L, .Label = "chr1", class = "factor"))
5: Rle(value, runLength(x))
6: (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("factor"), structure(function (values = logical(0), lengths = integer(0)) 
   standardGeneric("Rle"), generic = structure("Rle", package = "S4Vectors"), package = "S4Vectors", group = list(), valueClass = character(0), signature = "values", default = `\001NULL\001`, skeleton = (function (values = logical(0), 
       lengths = integer(0)) 
   stop("invalid call in method dispatch to 'Rle' (no default method)", domain = NA))(values, 
       lengths), class = structure("standardGeneric", package = "methods")), <environment>)
7: .findInheritedMethods(classes, fdef, mtable)
8: .newSignature(classes, fdef@signature)
9: .asS4(structure(as.character(classes)[i], class = .signatureClassName, names = as.character(names)[i], 
       package = pkgs))
10: asS4(object, TRUE, 0L)
11: structure(as.character(classes)[i], class = .signatureClassName, names = as.character(names)[i], 
       package = pkgs)
12: match(names(attrib), specials)
13: (function (x) 
   x$.self$finalize())(<environment>)

Error in signalCondition(e) : 
  no function to return from, jumping to top level
Calls: <Anonymous> -> .handleSimpleError -> h -> signalCondition
17. Error: block data fetch works (@test-data_fetch.R#4) -----------------------
attempt to apply non-function
1: GRanges(seqnames = "chr1", ranges = IRanges::IRanges(start = 1:10, width = 1), seqinfo = Seqinfo(seqnames = "chr1", 
       genome = "hcb")) at testthat/test-data_fetch.R:4
2: newGRanges("GRanges", seqnames = seqnames, ranges = ranges, strand = strand, mcols = DataFrame(..., 
       check.names = FALSE), seqlengths = seqlengths, seqinfo = seqinfo)
3: `runValue<-`(`*tmp*`, value = structure(1L, .Label = "chr1", class = "factor"))
4: `runValue<-`(`*tmp*`, value = structure(1L, .Label = "chr1", class = "factor"))
5: Rle(value, runLength(x))
6: (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("factor"), structure(function (values = logical(0), lengths = integer(0)) 
   standardGeneric("Rle"), generic = structure("Rle", package = "S4Vectors"), package = "S4Vectors", group = list(), valueClass = character(0), signature = "values", default = `\001NULL\001`, skeleton = (function (values = logical(0), 
       lengths = integer(0)) 
   stop("invalid call in method dispatch to 'Rle' (no default method)", domain = NA))(values, 
       lengths), class = structure("standardGeneric", package = "methods")), <environment>)
7: .findInheritedMethods(classes, fdef, mtable)
8: .newSignature(classes, fdef@signature)
9: .asS4(structure(as.character(classes)[i], class = .signatureClassName, names = as.character(names)[i], 
       package = pkgs))
10: asS4(object, TRUE, 0L)
11: structure(as.character(classes)[i], class = .signatureClassName, names = as.character(names)[i], 
       package = pkgs)
12: match(names(attrib), specials)
13: (function (x) 
   x$.self$finalize())(<environment>)

Error in signalCondition(e) : 
  no function to return from, jumping to top level
Calls: <Anonymous> -> .handleSimpleError -> h -> signalCondition
18. Error: block data fetch works (@test-data_fetch.R#4) -----------------------
attempt to apply non-function
1: GRanges(seqnames = "chr1", ranges = IRanges::IRanges(start = 1:10, width = 1), seqinfo = Seqinfo(seqnames = "chr1", 
       genome = "hcb")) at testthat/test-data_fetch.R:4
2: newGRanges("GRanges", seqnames = seqnames, ranges = ranges, strand = strand, mcols = DataFrame(..., 
       check.names = FALSE), seqlengths = seqlengths, seqinfo = seqinfo)
3: `runValue<-`(`*tmp*`, value = structure(1L, .Label = "chr1", class = "factor"))
4: `runValue<-`(`*tmp*`, value = structure(1L, .Label = "chr1", class = "factor"))
5: Rle(value, runLength(x))
6: (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("factor"), structure(function (values = logical(0), lengths = integer(0)) 
   standardGeneric("Rle"), generic = structure("Rle", package = "S4Vectors"), package = "S4Vectors", group = list(), valueClass = character(0), signature = "values", default = `\001NULL\001`, skeleton = (function (values = logical(0), 
       lengths = integer(0)) 
   stop("invalid call in method dispatch to 'Rle' (no default method)", domain = NA))(values, 
       lengths), class = structure("standardGeneric", package = "methods")), <environment>)
7: .findInheritedMethods(classes, fdef, mtable)
8: .newSignature(classes, fdef@signature)
9: .asS4(structure(as.character(classes)[i], class = .signatureClassName, names = as.character(names)[i], 
       package = pkgs))
10: asS4(object, TRUE, 0L)
11: structure(as.character(classes)[i], class = .signatureClassName, names = as.character(names)[i], 
       package = pkgs)
12: match(names(attrib), specials)
13: (function (x) 
   x$.self$finalize())(<environment>)

Error in signalCondition(e) : 
  no function to return from, jumping to top level
Calls: <Anonymous> -> .handleSimpleError -> h -> signalCondition
19. Error: block data fetch works (@test-data_fetch.R#4) -----------------------
attempt to apply non-function
1: GRanges(seqnames = "chr1", ranges = IRanges::IRanges(start = 1:10, width = 1), seqinfo = Seqinfo(seqnames = "chr1", 
       genome = "hcb")) at testthat/test-data_fetch.R:4
2: newGRanges("GRanges", seqnames = seqnames, ranges = ranges, strand = strand, mcols = DataFrame(..., 
       check.names = FALSE), seqlengths = seqlengths, seqinfo = seqinfo)
3: `runValue<-`(`*tmp*`, value = structure(1L, .Label = "chr1", class = "factor"))
4: `runValue<-`(`*tmp*`, value = structure(1L, .Label = "chr1", class = "factor"))
5: Rle(value, runLength(x))
6: (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("factor"), structure(function (values = logical(0), lengths = integer(0)) 
   standardGeneric("Rle"), generic = structure("Rle", package = "S4Vectors"), package = "S4Vectors", group = list(), valueClass = character(0), signature = "values", default = `\001NULL\001`, skeleton = (function (values = logical(0), 
       lengths = integer(0)) 
   stop("invalid call in method dispatch to 'Rle' (no default method)", domain = NA))(values, 
       lengths), class = structure("standardGeneric", package = "methods")), <environment>)
7: .findInheritedMethods(classes, fdef, mtable)
8: .newSignature(classes, fdef@signature)
9: .asS4(structure(as.character(classes)[i], class = .signatureClassName, names = as.character(names)[i], 
       package = pkgs))
10: asS4(object, TRUE, 0L)
11: structure(as.character(classes)[i], class = .signatureClassName, names = as.character(names)[i], 
       package = pkgs)
12: match(names(attrib), specials)
13: (function (x) 
   x$.self$finalize())(<environment>)

Error in signalCondition(e) : 
  no function to return from, jumping to top level
Calls: <Anonymous> -> .handleSimpleError -> h -> signalCondition
20. Error: block data fetch works (@test-data_fetch.R#4) -----------------------
attempt to apply non-function
1: GRanges(seqnames = "chr1", ranges = IRanges::IRanges(start = 1:10, width = 1), seqinfo = Seqinfo(seqnames = "chr1", 
       genome = "hcb")) at testthat/test-data_fetch.R:4
2: newGRanges("GRanges", seqnames = seqnames, ranges = ranges, strand = strand, mcols = DataFrame(..., 
       check.names = FALSE), seqlengths = seqlengths, seqinfo = seqinfo)
3: `runValue<-`(`*tmp*`, value = structure(1L, .Label = "chr1", class = "factor"))
4: `runValue<-`(`*tmp*`, value = structure(1L, .Label = "chr1", class = "factor"))
5: Rle(value, runLength(x))
6: (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("factor"), structure(function (values = logical(0), lengths = integer(0)) 
   standardGeneric("Rle"), generic = structure("Rle", package = "S4Vectors"), package = "S4Vectors", group = list(), valueClass = character(0), signature = "values", default = `\001NULL\001`, skeleton = (function (values = logical(0), 
       lengths = integer(0)) 
   stop("invalid call in method dispatch to 'Rle' (no default method)", domain = NA))(values, 
       lengths), class = structure("standardGeneric", package = "methods")), <environment>)
7: .findInheritedMethods(classes, fdef, mtable)
8: .newSignature(classes, fdef@signature)
9: .asS4(structure(as.character(classes)[i], class = .signatureClassName, names = as.character(names)[i], 
       package = pkgs))
10: asS4(object, TRUE, 0L)
11: structure(as.character(classes)[i], class = .signatureClassName, names = as.character(names)[i], 
       package = pkgs)
12: match(names(attrib), specials)
13: (function (x) 
   x$.self$finalize())(<environment>)

Error in signalCondition(e) : 
  no function to return from, jumping to top level
Calls: <Anonymous> -> .handleSimpleError -> h -> signalCondition
testthat results ================================================================
OK: 99 SKIPPED: 2 FAILED: 20
1. Error: block data fetch works (@test-data_fetch.R#4) 
2. Error: block data fetch works (@test-data_fetch.R#4) 
3. Error: block data fetch works (@test-data_fetch.R#4) 
4. Error: block data fetch works (@test-data_fetch.R#4) 
5. Error: block data fetch works (@test-data_fetch.R#4) 
6. Error: block data fetch works (@test-data_fetch.R#4) 
7. Error: block data fetch works (@test-data_fetch.R#4) 
8. Error: block data fetch works (@test-data_fetch.R#4) 
9. Error: block data fetch works (@test-data_fetch.R#4) 
1. ...

Error: testthat unit tests failed
Execution halted

* installing *source* package ‘epivizrData’ ...
** R
** inst
** preparing package for lazy loading
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded
* DONE (epivizrData)

name	user	system	elapsed
createMgr	0.042	0.000	0.043
register	0.463	0.008	0.474