{"action":"created","issue":{"url":"https://api.github.com/repos/BioinformaticsFMRP/TCGAbiolinks/issues/216","repository_url":"https://api.github.com/repos/BioinformaticsFMRP/TCGAbiolinks","labels_url":"https://api.github.com/repos/BioinformaticsFMRP/TCGAbiolinks/issues/216/labels{/name}","comments_url":"https://api.github.com/repos/BioinformaticsFMRP/TCGAbiolinks/issues/216/comments","events_url":"https://api.github.com/repos/BioinformaticsFMRP/TCGAbiolinks/issues/216/events","html_url":"https://github.com/BioinformaticsFMRP/TCGAbiolinks/issues/216","id":326699761,"node_id":"MDU6SXNzdWUzMjY2OTk3NjE=","number":216,"title":"Error in GDCquery","user":{"login":"joseluischinito","id":4474352,"node_id":"MDQ6VXNlcjQ0NzQzNTI=","avatar_url":"https://avatars2.githubusercontent.com/u/4474352?v=4","gravatar_id":"","url":"https://api.github.com/users/joseluischinito","html_url":"https://github.com/joseluischinito","followers_url":"https://api.github.com/users/joseluischinito/followers","following_url":"https://api.github.com/users/joseluischinito/following{/other_user}","gists_url":"https://api.github.com/users/joseluischinito/gists{/gist_id}","starred_url":"https://api.github.com/users/joseluischinito/starred{/owner}{/repo}","subscriptions_url":"https://api.github.com/users/joseluischinito/subscriptions","organizations_url":"https://api.github.com/users/joseluischinito/orgs","repos_url":"https://api.github.com/users/joseluischinito/repos","events_url":"https://api.github.com/users/joseluischinito/events{/privacy}","received_events_url":"https://api.github.com/users/joseluischinito/received_events","type":"User","site_admin":false},"labels":[],"state":"closed","locked":false,"assignee":null,"assignees":[],"milestone":null,"comments":19,"created_at":"2018-05-26T01:32:09Z","updated_at":"2018-06-08T12:07:47Z","closed_at":"2018-06-05T02:09:42Z","author_association":"NONE","body":"Hi\r\n\r\nWhen I run following things in R it makes error.\r\n\r\nquery.exp <- GDCquery(project = \"TCGA-KIRC\", legacy = TRUE, data.category = \"Gene expression\", data.type = \"Gene expression quantification\", platform = \"Illumina HiSeq\", file.type = \"results\",           experimental.strategy = \"RNA-Seq\", sample.type = c(\"Primary solid Tumor\",\"Solid Tissue Normal\"))\r\n\r\n\r\n```\r\n--------------------------------------\r\no GDCquery: Searching in GDC database\r\n--------------------------------------\r\nGenome of reference: hg19\r\n--------------------------------------------\r\noo Accessing GDC. This might take a while...\r\n--------------------------------------------\r\nooo Project: TCGA-KIRC\r\nError:  Error in getURL(url, fromJSON, timeout(600), simplifyDataFrame = TRUE): 'getURL()' failed:\r\n  URL: https://gdc-api.nci.nih.gov/legacy/files/?pretty=true&expand=cases.samples.portions.analytes.aliquots,cases.project,center,analysis&size=7757&filters=%7B%22op%22:%22and%22,%22content%22:[%7B%22op%22:%22in%22,%22content%22:%7B%22field%22:%22cases.project.project_id%22,%22value%22:[%22TCGA-KIRC%22]%7D%7D,%7B%22op%22:%22in%22,%22content%22:%7B%22field%22:%22files.data_category%22,%22value%22:[%22Gene%20expression%22]%7D%7D,%7B%22op%22:%22in%22,%22content%22:%7B%22field%22:%22files.data_type%22,%22value%22:[%22Gene%20expression%20quantification%22]%7D%7D,%7B%22op%22:%22in%22,%22content%22:%7B%22field%22:%22files.platform%22,%22value%22:[%22Illumina%20HiSeq%22]%7D%7D]%7D&format=JSON\r\n  error: Failure when receiving data from the peer\r\n\r\nWe will retry to access GDC!\r\nError in if (json$data$pagination$count == 0) { : \r\n  argument is of length zero\r\n\r\n```\r\n\r\nYesterday it executed well\r\n\r\n"},"comment":{"url":"https://api.github.com/repos/BioinformaticsFMRP/TCGAbiolinks/issues/comments/395741242","html_url":"https://github.com/BioinformaticsFMRP/TCGAbiolinks/issues/216#issuecomment-395741242","issue_url":"https://api.github.com/repos/BioinformaticsFMRP/TCGAbiolinks/issues/216","id":395741242,"node_id":"MDEyOklzc3VlQ29tbWVudDM5NTc0MTI0Mg==","user":{"login":"Melkiades","id":11279768,"node_id":"MDQ6VXNlcjExMjc5NzY4","avatar_url":"https://avatars2.githubusercontent.com/u/11279768?v=4","gravatar_id":"","url":"https://api.github.com/users/Melkiades","html_url":"https://github.com/Melkiades","followers_url":"https://api.github.com/users/Melkiades/followers","following_url":"https://api.github.com/users/Melkiades/following{/other_user}","gists_url":"https://api.github.com/users/Melkiades/gists{/gist_id}","starred_url":"https://api.github.com/users/Melkiades/starred{/owner}{/repo}","subscriptions_url":"https://api.github.com/users/Melkiades/subscriptions","organizations_url":"https://api.github.com/users/Melkiades/orgs","repos_url":"https://api.github.com/users/Melkiades/repos","events_url":"https://api.github.com/users/Melkiades/events{/privacy}","received_events_url":"https://api.github.com/users/Melkiades/received_events","type":"User","site_admin":false},"created_at":"2018-06-08T12:07:47Z","updated_at":"2018-06-08T12:07:47Z","author_association":"CONTRIBUTOR","body":"That error can be resolved after restarting the R session and it is independent from `TCGAbiolinks` (it is `data.table` as you can see. Here, there is a similar [problem-solution](https://github.com/lme4/lme4/issues/407)."}}
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