{"action":"created","issue":{"url":"https://api.github.com/repos/lianos/multiGSEA/issues/17","repository_url":"https://api.github.com/repos/lianos/multiGSEA","labels_url":"https://api.github.com/repos/lianos/multiGSEA/issues/17/labels{/name}","comments_url":"https://api.github.com/repos/lianos/multiGSEA/issues/17/comments","events_url":"https://api.github.com/repos/lianos/multiGSEA/issues/17/events","html_url":"https://github.com/lianos/multiGSEA/issues/17","id":427058084,"node_id":"MDU6SXNzdWU0MjcwNTgwODQ=","number":17,"title":"Failing tests","user":{"login":"mukhyala","id":1018689,"node_id":"MDQ6VXNlcjEwMTg2ODk=","avatar_url":"https://avatars3.githubusercontent.com/u/1018689?v=4","gravatar_id":"","url":"https://api.github.com/users/mukhyala","html_url":"https://github.com/mukhyala","followers_url":"https://api.github.com/users/mukhyala/followers","following_url":"https://api.github.com/users/mukhyala/following{/other_user}","gists_url":"https://api.github.com/users/mukhyala/gists{/gist_id}","starred_url":"https://api.github.com/users/mukhyala/starred{/owner}{/repo}","subscriptions_url":"https://api.github.com/users/mukhyala/subscriptions","organizations_url":"https://api.github.com/users/mukhyala/orgs","repos_url":"https://api.github.com/users/mukhyala/repos","events_url":"https://api.github.com/users/mukhyala/events{/privacy}","received_events_url":"https://api.github.com/users/mukhyala/received_events","type":"User","site_admin":false},"labels":[],"state":"closed","locked":false,"assignee":null,"assignees":[],"milestone":null,"comments":3,"created_at":"2019-03-29T15:57:08Z","updated_at":"2019-04-01T17:30:10Z","closed_at":"2019-03-30T06:59:39Z","author_association":"NONE","body":"Hi Steve,\r\n\r\nWe use the master branch of multiGSEA (v0.11.1) which does not pass tests on R 3.5.1 using Bioc 3.8. Would you be able to fix these tests? Any advice would be great.\r\n\r\n`\r\n> library(multiGSEA)\r\nLoading required package: edgeR\r\nLoading required package: limma\r\nRegistered S3 methods overwritten by 'ggplot2':\r\n  method         from \r\n  [.quosures     rlang\r\n  c.quosures     rlang\r\n  print.quosures rlang\r\nWarning messages:\r\n1: replacing previous import ‘ggplot2::last_plot’ by ‘plotly::last_plot’ when loading ‘multiGSEA’ \r\n2: replacing previous import ‘data.table::melt’ by ‘reshape2::melt’ when loading ‘multiGSEA’ \r\n3: replacing previous import ‘data.table::dcast’ by ‘reshape2::dcast’ when loading ‘multiGSEA’ \r\n4: replacing previous import ‘plotly::filter’ by ‘stats::filter’ when loading ‘multiGSEA’ \r\n> packageDescription('multiGSEA')\r\nPackage: multiGSEA\r\nType: Package\r\nTitle: A unified interface to a plethora of gene set enrichment\r\n        analysis methods\r\nVersion: 0.11.1\r\nAuthors@R: c( person(\"Steve\", \"Lianoglou\", , \"slianoglou@gmail.com\",\r\n        c(\"aut\", \"cre\")), person(\"Genentech\", role = c(\"cph\", \"fnd\")),\r\n        person(\"Denali Therapeutics\", role = c(\"fnd\")) )\r\nDescription: Provides a unified interface to orchestrate a plethora of\r\n        GSEA methods over a contrast of interest as well as single\r\n        sample gene set scoring methods. This package also provides\r\n        robust interactive tools to explore GSEA results.\r\nDepends: edgeR (>= 3.18.1)\r\nImports: BiocGenerics, BiocParallel, Biobase (>= 2.24.0), circlize,\r\n        ComplexHeatmap, ggplot2 (>= 2.2.0), GSEABase, GSVA, data.table\r\n        (>= 1.10.4), magrittr, Matrix, matrixStats, methods, plotly (>=\r\n        4.7.0), reshape2, viridis, limma\r\nSuggests: AnnotationDbi, BiocStyle, DESeq2, dplyr, dtplyr,\r\n        GeneSetDb.MSigDB.Hsapiens.v61, GeneSetDb.MSigDB.Mmusculus.v61,\r\n        fgsea, GO.db, goseq, KernSmooth, knitr, org.Hs.eg.db,\r\n        org.Mm.eg.db, PANTHER.db (>= 1.0.3), reactome.db,\r\n        SummarizedExperiment, statmod, testthat, webshot\r\nVignetteBuilder: knitr\r\nLicense: MIT + file LICENSE\r\nEncoding: UTF-8\r\nLazyData: true\r\nCollate: 'AllClasses.R' 'AllGenerics.R' 'GeneSetDb-class.R' .....\r\nRoxygenNote: 6.0.1.9000\r\nbiocViews: Pathways, GeneSetEnrichment, DifferentialExpression, GO,\r\n        RNASeq\r\nNeedsCompilation: no\r\nPackaged: 2019-03-28 16:47:55 UTC; mukhyala\r\nAuthor: Steve Lianoglou [aut, cre], Genentech [cph, fnd], Denali\r\n        Therapeutics [fnd]\r\nMaintainer: Steve Lianoglou <slianoglou@gmail.com>\r\nBuilt: R 3.6.0; ; 2019-03-28 20:41:18 UTC; unix\r\n\r\n-- File: /***/Rlib/3.5.1-Bioc-3.8-test/multiGSEA/Meta/package.rds \r\n> library(devtools)\r\n> test('.')\r\nLoading multiGSEA\r\nCreating a generic function for ‘nrow’ from package ‘base’ in package ‘multiGSEA’\r\n\r\nAttaching package: ‘testthat’\r\n\r\nThe following objects are masked from ‘package:devtools’:\r\n\r\n    setup, test_file\r\n\r\n\r\nAttaching package: ‘magrittr’\r\n\r\nThe following objects are masked from ‘package:testthat’:\r\n\r\n    equals, is_less_than, not\r\n\r\ndata.table 1.12.0  Latest news: r-datatable.com\r\n\r\nAttaching package: ‘dplyr’\r\n\r\nThe following objects are masked from ‘package:data.table’:\r\n\r\n    between, first, last\r\n\r\nThe following object is masked from ‘package:testthat’:\r\n\r\n    matches\r\n\r\nThe following objects are masked from ‘package:stats’:\r\n\r\n    filter, lag\r\n\r\nThe following objects are masked from ‘package:base’:\r\n\r\n    intersect, setdiff, setequal, union\r\n\r\nTesting multiGSEA\r\n✔ | OK F W S | Context\r\n✔ |  0     1 | Testing GSEA results in adversarial situations\r\n────────────────────────────────────────────────────────────────────────────────\r\ntest-adversarial-gsea.R:4: skip: Gene Sets with logFCs in oppossite extremes\r\nEmpty test\r\n────────────────────────────────────────────────────────────────────────────────\r\n✔ | 15       | calculateIndividualLogFC [138.9 s]\r\n✔ |  9       | camera [141.1 s]\r\n✔ |  2       | Using DGEList's as input [46.7 s]\r\n✔ |  9       | fgsea [81.1 s]\r\n✔ |  6       | fry [65.1 s]\r\n✔ | 1586     1 | GeneSetDb [1013.7 s]\r\n────────────────────────────────────────────────────────────────────────────────\r\ntest-GeneSetDb.R:470: skip: GeneSetDb indexing `[` works\r\nEmpty test\r\n────────────────────────────────────────────────────────────────────────────────\r\n✔ |  1       | geneSetsStats [106.4 s]\r\n✔ |  6       | geneSetSummaryByGenes [107.5 s]\r\n✖ |  0 1     | geneSetTest [64.0 s]\r\n────────────────────────────────────────────────────────────────────────────────\r\ntest-geneSetTest.R:21: error: geneSetTest matches re-implememtation\r\nUnexpected geneset ordering in `geneSetTest` result\r\n1: result(mg, \"geneSetTest\") at /***/multiGSEA/tests/testthat/test-geneSetTest.R:21\r\n2: (function() {\r\n       fnname <- sub(\"\\\\..*$\", \"\", name)\r\n       fnname <- paste0(\"mgres.\", fnname)\r\n       fnfetch <- getFunction(fnname)\r\n       r <- fnfetch(x@results[[name]], geneSetDb(x))\r\n       kosher <- all.equal(out[, key(out), with = FALSE], r[, key(out), with = FALSE])[1L]\r\n       if (!isTRUE(kosher)) {\r\n           stop(\"Unexpected geneset ordering in `\", name, \"` result\")\r\n       }\r\n       if (!all(c(\"pval\", \"padj\") %in% colnames(r))) {\r\n           stop(fnname, \" does not provide pval and/or padj column\")\r\n       }\r\n       if (stats.only) {\r\n           res.cols <- names(r)[grepl(\"^(pval\\\\.?|padj\\\\.?)\", names(r))]\r\n       }\r\n       else {\r\n           res.cols <- setdiff(names(r), names(out))\r\n       }\r\n       r <- r[, res.cols, with = FALSE]\r\n       r\r\n   })() at /***/multiGSEA/R/MultiGSEAResult-methods.R:299\r\n3: stop(\"Unexpected geneset ordering in `\", name, \"` result\") at /***/projects/multiGSEA/R/MultiGSEAResult-methods.R:316\r\n────────────────────────────────────────────────────────────────────────────────\r\n✔ | 10       | goseq [163.1 s]\r\n✖ |  0 1     | Hyper Geometric Test [11.8 s]\r\n────────────────────────────────────────────────────────────────────────────────\r\ntest-hyperGeometricTest.R:30: error: hyperGeometricTest performs like do.hyperGeometricTest performs\r\nUnexpected geneset ordering in `hyperGeometricTest` result\r\n1: results(mg) at /***/multiGSEA/tests/testthat/test-hyperGeometricTest.R:30\r\n2: result(x, name, stats.only, rank.by, add.suffix, as.dt = TRUE) at /***/multiGSEA/R/MultiGSEAResult-methods.R:393\r\n3: (function() {\r\n       fnname <- sub(\"\\\\..*$\", \"\", name)\r\n       fnname <- paste0(\"mgres.\", fnname)\r\n       fnfetch <- getFunction(fnname)\r\n       r <- fnfetch(x@results[[name]], geneSetDb(x))\r\n       kosher <- all.equal(out[, key(out), with = FALSE], r[, key(out), with = FALSE])[1L]\r\n       if (!isTRUE(kosher)) {\r\n           stop(\"Unexpected geneset ordering in `\", name, \"` result\")\r\n       }\r\n       if (!all(c(\"pval\", \"padj\") %in% colnames(r))) {\r\n           stop(fnname, \" does not provide pval and/or padj column\")\r\n       }\r\n       if (stats.only) {\r\n           res.cols <- names(r)[grepl(\"^(pval\\\\.?|padj\\\\.?)\", names(r))]\r\n       }\r\n       else {\r\n           res.cols <- setdiff(names(r), names(out))\r\n       }\r\n       r <- r[, res.cols, with = FALSE]\r\n       r\r\n   })() at /***/multiGSEA/R/MultiGSEAResult-methods.R:299\r\n4: stop(\"Unexpected geneset ordering in `\", name, \"` result\") at /***/multiGSEA/R/MultiGSEAResult-methods.R:316\r\n────────────────────────────────────────────────────────────────────────────────\r\n✔ |  0       | Interactive Plotting\r\n✔ |  5       | Pass-through logFC GSEA method [39.1 s]\r\n✔ |  3       | multiGSEA [30.1 s]\r\n✔ |  4     1 | MultiGSEAResult [14.5 s]\r\n────────────────────────────────────────────────────────────────────────────────\r\ntest-MultiGSEAResult.R:3: skip: subset.MultiGSEAResult works\r\nEmpty test\r\n────────────────────────────────────────────────────────────────────────────────\r\n✔ |  0       | PANTHER.db\r\n✔ |  4       | roast [13.0 s]\r\n✔ |  9       | romer [41.1 s]\r\n✔ | 10       | Single Sample Gene Set Scoring [115.1 s]\r\n✖ |  6 2     | Errors submitted by users [23.3 s]\r\n────────────────────────────────────────────────────────────────────────────────\r\ntest-users.R:19: failure: multiGSEA fails with a 1-geneset GeneSetDb\r\n`printed` inherits from `NULL` not `character`.\r\n\r\ntest-users.R:23: error: multiGSEA fails with a 1-geneset GeneSetDb\r\nUnexpected geneset ordering in `geneSetTest` result\r\n1: result(mg, method) at /***/projects/multiGSEA/tests/testthat/test-users.R:23\r\n2: (function() {\r\n       fnname <- sub(\"\\\\..*$\", \"\", name)\r\n       fnname <- paste0(\"mgres.\", fnname)\r\n       fnfetch <- getFunction(fnname)\r\n       r <- fnfetch(x@results[[name]], geneSetDb(x))\r\n       kosher <- all.equal(out[, key(out), with = FALSE], r[, key(out), with = FALSE])[1L]\r\n       if (!isTRUE(kosher)) {\r\n           stop(\"Unexpected geneset ordering in `\", name, \"` result\")\r\n       }\r\n       if (!all(c(\"pval\", \"padj\") %in% colnames(r))) {\r\n           stop(fnname, \" does not provide pval and/or padj column\")\r\n       }\r\n       if (stats.only) {\r\n           res.cols <- names(r)[grepl(\"^(pval\\\\.?|padj\\\\.?)\", names(r))]\r\n       }\r\n       else {\r\n           res.cols <- setdiff(names(r), names(out))\r\n       }\r\n       r <- r[, res.cols, with = FALSE]\r\n       r\r\n   })() at /***/multiGSEA/R/MultiGSEAResult-methods.R:299\r\n3: stop(\"Unexpected geneset ordering in `\", name, \"` result\") at /***/multiGSEA/R/MultiGSEAResult-methods.R:316\r\n────────────────────────────────────────────────────────────────────────────────\r\n\r\n══ Results ═════════════════════════════════════════════════════════════════════\r\nDuration: 2216.8 s\r\n\r\nOK:       1685\r\nFailed:   4\r\nWarnings: 0\r\nSkipped:  3\r\nWarning messages:\r\n1: replacing previous import ‘ggplot2::last_plot’ by ‘plotly::last_plot’ when loading ‘multiGSEA’ \r\n2: replacing previous import ‘data.table::melt’ by ‘reshape2::melt’ when loading ‘multiGSEA’ \r\n3: replacing previous import ‘data.table::dcast’ by ‘reshape2::dcast’ when loading ‘multiGSEA’ \r\n4: replacing previous import ‘plotly::filter’ by ‘stats::filter’ when loading ‘multiGSEA’ \r\n`\r\n\r\nThanks,\r\n-Kiran"},"comment":{"url":"https://api.github.com/repos/lianos/multiGSEA/issues/comments/478671340","html_url":"https://github.com/lianos/multiGSEA/issues/17#issuecomment-478671340","issue_url":"https://api.github.com/repos/lianos/multiGSEA/issues/17","id":478671340,"node_id":"MDEyOklzc3VlQ29tbWVudDQ3ODY3MTM0MA==","user":{"login":"mukhyala","id":1018689,"node_id":"MDQ6VXNlcjEwMTg2ODk=","avatar_url":"https://avatars3.githubusercontent.com/u/1018689?v=4","gravatar_id":"","url":"https://api.github.com/users/mukhyala","html_url":"https://github.com/mukhyala","followers_url":"https://api.github.com/users/mukhyala/followers","following_url":"https://api.github.com/users/mukhyala/following{/other_user}","gists_url":"https://api.github.com/users/mukhyala/gists{/gist_id}","starred_url":"https://api.github.com/users/mukhyala/starred{/owner}{/repo}","subscriptions_url":"https://api.github.com/users/mukhyala/subscriptions","organizations_url":"https://api.github.com/users/mukhyala/orgs","repos_url":"https://api.github.com/users/mukhyala/repos","events_url":"https://api.github.com/users/mukhyala/events{/privacy}","received_events_url":"https://api.github.com/users/mukhyala/received_events","type":"User","site_admin":false},"created_at":"2019-04-01T17:30:10Z","updated_at":"2019-04-01T17:30:10Z","author_association":"NONE","body":"Thanks for a quick fix Steve! \r\nHaunting ghosts would be an understatement! I've even heard of someone missing out on watching 168 movies on airplanes due to exploring data with FacileExplorer using the local installation. \r\nWill cost you a beer@F&L to learn more though ..."}}
{"actor":{"display_login":"mukhyala"}}