{"action":"created","issue":{"url":"https://api.github.com/repos/joey711/phyloseq/issues/443","labels_url":"https://api.github.com/repos/joey711/phyloseq/issues/443/labels{/name}","comments_url":"https://api.github.com/repos/joey711/phyloseq/issues/443/comments","events_url":"https://api.github.com/repos/joey711/phyloseq/issues/443/events","html_url":"https://github.com/joey711/phyloseq/issues/443","id":60752024,"number":443,"title":"importing BIOM file","user":{"login":"alejorojas2","id":5539247,"avatar_url":"https://avatars.githubusercontent.com/u/5539247?v=3","gravatar_id":"","url":"https://api.github.com/users/alejorojas2","html_url":"https://github.com/alejorojas2","followers_url":"https://api.github.com/users/alejorojas2/followers","following_url":"https://api.github.com/users/alejorojas2/following{/other_user}","gists_url":"https://api.github.com/users/alejorojas2/gists{/gist_id}","starred_url":"https://api.github.com/users/alejorojas2/starred{/owner}{/repo}","subscriptions_url":"https://api.github.com/users/alejorojas2/subscriptions","organizations_url":"https://api.github.com/users/alejorojas2/orgs","repos_url":"https://api.github.com/users/alejorojas2/repos","events_url":"https://api.github.com/users/alejorojas2/events{/privacy}","received_events_url":"https://api.github.com/users/alejorojas2/received_events","type":"User","site_admin":false},"labels":[{"url":"https://api.github.com/repos/joey711/phyloseq/labels/Feature","name":"Feature","color":"02e10c"}],"state":"open","locked":false,"assignee":null,"milestone":null,"comments":31,"created_at":"2015-03-12T00:17:58Z","updated_at":"2015-11-06T15:02:59Z","closed_at":null,"body":"Hi Joey711,\r\n\r\nI have been trying to import a biom file that I generated with qiime, the file is binary file, it seems that is new format for this kind of files, then when trying to work with it in R I get this error:\r\n\r\nThis is my code so far:\r\n```\r\n#Importing with BIOM function\r\nbiom_file <- \"./COI_seed_otu_table.biom\"\r\ntree_file <- \"./COI_fasttree_usearch.tre\"\r\n\r\nCOI_data <- import_biom(biom_file)\r\n```\r\nCOI_data <- import_biom(biom_file)\r\nError in nchar(content) : invalid multibyte string 1\r\n\r\n```\r\n#importing with qiime function\r\nCOI_data <- import_qiime(biom_file)\r\n```\r\n\r\nCOI_data <- import_qiime(BIOMfilename = biom_file)\r\nError in arglist[sapply(arglist, is.component.class)] : \r\n  invalid subscript type 'list'\r\n\r\nMaybe I am missing something or should I use an older version of BIOM file?\r\n"},"comment":{"url":"https://api.github.com/repos/joey711/phyloseq/issues/comments/154431691","html_url":"https://github.com/joey711/phyloseq/issues/443#issuecomment-154431691","issue_url":"https://api.github.com/repos/joey711/phyloseq/issues/443","id":154431691,"user":{"login":"jnpaulson","id":3039619,"avatar_url":"https://avatars.githubusercontent.com/u/3039619?v=3","gravatar_id":"","url":"https://api.github.com/users/jnpaulson","html_url":"https://github.com/jnpaulson","followers_url":"https://api.github.com/users/jnpaulson/followers","following_url":"https://api.github.com/users/jnpaulson/following{/other_user}","gists_url":"https://api.github.com/users/jnpaulson/gists{/gist_id}","starred_url":"https://api.github.com/users/jnpaulson/starred{/owner}{/repo}","subscriptions_url":"https://api.github.com/users/jnpaulson/subscriptions","organizations_url":"https://api.github.com/users/jnpaulson/orgs","repos_url":"https://api.github.com/users/jnpaulson/repos","events_url":"https://api.github.com/users/jnpaulson/events{/privacy}","received_events_url":"https://api.github.com/users/jnpaulson/received_events","type":"User","site_admin":false},"created_at":"2015-11-06T15:02:58Z","updated_at":"2015-11-06T15:02:58Z","body":"@mafed interesting - can you perhaps post this in the biomformat package: https://github.com/joey711/biomformat/issues and i'll go ahead and fix this"}}