{"action":"opened","issue":{"url":"https://api.github.com/repos/LTLA/csaw/issues/2","repository_url":"https://api.github.com/repos/LTLA/csaw","labels_url":"https://api.github.com/repos/LTLA/csaw/issues/2/labels{/name}","comments_url":"https://api.github.com/repos/LTLA/csaw/issues/2/comments","events_url":"https://api.github.com/repos/LTLA/csaw/issues/2/events","html_url":"https://github.com/LTLA/csaw/issues/2","id":144546514,"number":2,"title":"csaw user guide quick start script throws error","user":{"login":"endrebak","id":17778898,"avatar_url":"https://avatars.githubusercontent.com/u/17778898?v=3","gravatar_id":"","url":"https://api.github.com/users/endrebak","html_url":"https://github.com/endrebak","followers_url":"https://api.github.com/users/endrebak/followers","following_url":"https://api.github.com/users/endrebak/following{/other_user}","gists_url":"https://api.github.com/users/endrebak/gists{/gist_id}","starred_url":"https://api.github.com/users/endrebak/starred{/owner}{/repo}","subscriptions_url":"https://api.github.com/users/endrebak/subscriptions","organizations_url":"https://api.github.com/users/endrebak/orgs","repos_url":"https://api.github.com/users/endrebak/repos","events_url":"https://api.github.com/users/endrebak/events{/privacy}","received_events_url":"https://api.github.com/users/endrebak/received_events","type":"User","site_admin":false},"labels":[],"state":"open","locked":false,"assignee":null,"milestone":null,"comments":0,"created_at":"2016-03-30T10:46:13Z","updated_at":"2016-03-30T10:46:13Z","closed_at":null,"body":"I dunno if this is related to the csaw code, if not then just close.\r\n\r\nIn the quickstart guide, you first load csaw, then edgeR to use the aveLogCPM function.\r\n\r\nThis is not working for me; I get the error below:\r\n\r\n```\r\nlibrary(csaw);library(edgeR)\r\nLoading required package: GenomicRanges\r\nLoading required package: BiocGenerics\r\nLoading required package: parallel\r\n\r\nAttaching package: ‘BiocGenerics’\r\n\r\nThe following objects are masked from ‘package:parallel’:\r\n\r\n    clusterApply, clusterApplyLB, clusterCall, clusterEvalQ,\r\n    clusterExport, clusterMap, parApply, parCapply, parLapply,\r\n    parLapplyLB, parRapply, parSapply, parSapplyLB\r\n\r\nThe following objects are masked from ‘package:stats’:\r\n\r\n    IQR, mad, xtabs\r\n\r\nThe following objects are masked from ‘package:base’:\r\n\r\n    anyDuplicated, append, as.data.frame, as.vector, cbind, colnames,\r\n    do.call, duplicated, eval, evalq, Filter, Find, get, grep, grepl,\r\n    intersect, is.unsorted, lapply, lengths, Map, mapply, match, mget,\r\n    order, paste, pmax, pmax.int, pmin, pmin.int, Position, rank,\r\n    rbind, Reduce, rownames, sapply, setdiff, sort, table, tapply,\r\n    union, unique, unlist, unsplit\r\n\r\nLoading required package: S4Vectors\r\nLoading required package: stats4\r\nLoading required package: IRanges\r\nLoading required package: GenomeInfoDb\r\nLoading required package: SummarizedExperiment\r\nLoading required package: Biobase\r\nWelcome to Bioconductor\r\n\r\n    Vignettes contain introductory material; view with\r\n    'browseVignettes()'. To cite Bioconductor, see\r\n    'citation(\"Biobase\")', and for packages 'citation(\"pkgname\")'.\r\n\r\nLoading required package: limma\r\nError in unloadNamespace(package) :\r\n  namespace ‘limma’ is imported by ‘csaw’, ‘edgeR’ so cannot be unloaded\r\nError in library(pkg, character.only = TRUE, logical.return = TRUE, lib.loc = lib.loc,  :\r\n  Package ‘limma’ version 3.27.4 cannot be unloaded\r\n```"}}