{"action":"created","issue":{"url":"https://api.github.com/repos/lgatto/MSnbase/issues/138","repository_url":"https://api.github.com/repos/lgatto/MSnbase","labels_url":"https://api.github.com/repos/lgatto/MSnbase/issues/138/labels{/name}","comments_url":"https://api.github.com/repos/lgatto/MSnbase/issues/138/comments","events_url":"https://api.github.com/repos/lgatto/MSnbase/issues/138/events","html_url":"https://github.com/lgatto/MSnbase/issues/138","id":168033780,"number":138,"title":"Randomly failing unit tests","user":{"login":"jotsetung","id":5506112,"avatar_url":"https://avatars.githubusercontent.com/u/5506112?v=3","gravatar_id":"","url":"https://api.github.com/users/jotsetung","html_url":"https://github.com/jotsetung","followers_url":"https://api.github.com/users/jotsetung/followers","following_url":"https://api.github.com/users/jotsetung/following{/other_user}","gists_url":"https://api.github.com/users/jotsetung/gists{/gist_id}","starred_url":"https://api.github.com/users/jotsetung/starred{/owner}{/repo}","subscriptions_url":"https://api.github.com/users/jotsetung/subscriptions","organizations_url":"https://api.github.com/users/jotsetung/orgs","repos_url":"https://api.github.com/users/jotsetung/repos","events_url":"https://api.github.com/users/jotsetung/events{/privacy}","received_events_url":"https://api.github.com/users/jotsetung/received_events","type":"User","site_admin":false},"labels":[{"url":"https://api.github.com/repos/lgatto/MSnbase/labels/MSnbase2","name":"MSnbase2","color":"bfdadc"}],"state":"open","locked":false,"assignee":null,"assignees":[],"milestone":null,"comments":11,"created_at":"2016-07-28T07:47:12Z","updated_at":"2016-08-01T16:25:31Z","closed_at":null,"body":"@lgatto are you also getting failing unit tests e.g. in *test_equalMSnExp.R*? What really puzzles me is that I don't get any errors when I run this file selectively with `test_file(\"test_equalMSnExps.R\")` or if I run all tests using `test_dir(\".\")`, but I get errors when I use `source(\"testthat.R\")`:\r\n\r\n```{r}\r\n1. Error: Equality function (@test_equalMSnExps.R#12) --------------------------\r\nno function to return from, jumping to top level\r\n1: expect_true(all.equal(inmem1, ondisk1)) at testthat/test_equalMSnExps.R:12\r\n2: expect(identical(as.vector(object), TRUE), sprintf(\"%s isn't true.\", lab), info = info)\r\n3: as.expectation(exp, ..., srcref = srcref)\r\n4: identical(as.vector(object), TRUE)\r\n5: as.vector(object)\r\n6: all.equal(inmem1, ondisk1)\r\n7: all.equal(inmem1, ondisk1)\r\n8: equalMSnExps(target, current, ...)\r\n9: spectra(ondisk)\r\n10: spectra(ondisk)\r\n11: .local(object, ...)\r\n12: spectrapply(object, BPPARAM = BPPARAM)\r\n13: bplapply(fDataPerFile, FUN = .applyFun2SpectraOfFileMulti, filenames = fNames, queue = theQ, \r\n       APPLYFUN = FUN, BPPARAM = BPPARAM, ...)\r\n14: bplapply(fDataPerFile, FUN = .applyFun2SpectraOfFileMulti, filenames = fNames, queue = theQ, \r\n       APPLYFUN = FUN, BPPARAM = BPPARAM, ...)\r\n15: lapply(X, FUN, ...)\r\n16: FUN(X[[i]], ...)\r\n17: withCallingHandlers({\r\n       tryCatch({\r\n           FUN(...)\r\n       }, error = handle_error)\r\n   }, warning = handle_warning)\r\n18: tryCatch({\r\n       FUN(...)\r\n   }, error = handle_error)\r\n19: tryCatchList(expr, classes, parentenv, handlers)\r\n20: tryCatchOne(expr, names, parentenv, handlers[[1L]])\r\n21: doTryCatch(return(expr), name, parentenv, handler)\r\n22: FUN(...)\r\n23: lengths(allSpect)\r\n24: (function (classes, fdef, mtable) \r\n   {\r\n       methods <- .findInheritedMethods(classes, fdef, mtable)\r\n       if (length(methods) == 1L) \r\n           return(methods[[1L]])\r\n       else if (length(methods) == 0L) {\r\n           cnames <- paste0(\"\\\"\", vapply(classes, as.character, \"\"), \"\\\"\", collapse = \", \")\r\n           stop(gettextf(\"unable to find an inherited method for function %s for signature %s\", \r\n               sQuote(fdef@generic), sQuote(cnames)), domain = NA)\r\n       }\r\n       else stop(\"Internal error in finding inherited methods; didn't return a unique method\", \r\n           domain = NA)\r\n   })(list(\"list\"), structure(function (x, use.names = TRUE) \r\n   standardGeneric(\"lengths\"), generic = structure(\"lengths\", package = \"BiocGenerics\"), package = \"BiocGenerics\", group = list(), valueClass = character(0), signature = \"x\", default = structure(function (x, \r\n       use.names = TRUE) \r\n   .Internal(lengths(x, use.names)), target = structure(\"ANY\", class = structure(\"signature\", package = \"methods\"), .Names = \"x\", package = \"methods\"), defined = structure(\"ANY\", class = structure(\"signature\", package = \"methods\"), .Names = \"x\", package = \"methods\"), generic = structure(\"lengths\", package = \"base\"), class = structure(\"derivedDefaultMethod\", package = \"methods\")), skeleton = (structure(function (x, \r\n       use.names = TRUE) \r\n   .Internal(lengths(x, use.names)), target = structure(\"ANY\", class = structure(\"signature\", package = \"methods\"), .Names = \"x\", package = \"methods\"), defined = structure(\"ANY\", class = structure(\"signature\", package = \"methods\"), .Names = \"x\", package = \"methods\"), generic = structure(\"lengths\", package = \"base\"), class = structure(\"derivedDefaultMethod\", package = \"methods\")))(x, \r\n       use.names), class = structure(\"standardGeneric\", package = \"methods\")), <environment>)\r\n25: .findInheritedMethods(classes, fdef, mtable)\r\n26: .newSignature(classes, fdef@signature)\r\n27: packageSlot(classes)\r\n28: (function (x) \r\n   x$.self$finalize())(<environment>)\r\n\r\n```\r\n\r\nI'll investigate further, but eventually you have already a solution."},"comment":{"url":"https://api.github.com/repos/lgatto/MSnbase/issues/comments/236631626","html_url":"https://github.com/lgatto/MSnbase/issues/138#issuecomment-236631626","issue_url":"https://api.github.com/repos/lgatto/MSnbase/issues/138","id":236631626,"user":{"login":"lgatto","id":384198,"avatar_url":"https://avatars.githubusercontent.com/u/384198?v=3","gravatar_id":"","url":"https://api.github.com/users/lgatto","html_url":"https://github.com/lgatto","followers_url":"https://api.github.com/users/lgatto/followers","following_url":"https://api.github.com/users/lgatto/following{/other_user}","gists_url":"https://api.github.com/users/lgatto/gists{/gist_id}","starred_url":"https://api.github.com/users/lgatto/starred{/owner}{/repo}","subscriptions_url":"https://api.github.com/users/lgatto/subscriptions","organizations_url":"https://api.github.com/users/lgatto/orgs","repos_url":"https://api.github.com/users/lgatto/repos","events_url":"https://api.github.com/users/lgatto/events{/privacy}","received_events_url":"https://api.github.com/users/lgatto/received_events","type":"User","site_admin":false},"created_at":"2016-08-01T16:25:31Z","updated_at":"2016-08-01T16:25:31Z","body":"I have added `tests/testthat/fails.md` file in the `MSnbase2` branch, to document more systematically the errors and try to identify a pattern. "}}
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