{"action":"created","issue":{"url":"https://api.github.com/repos/seandavi/GEOquery/issues/49","repository_url":"https://api.github.com/repos/seandavi/GEOquery","labels_url":"https://api.github.com/repos/seandavi/GEOquery/issues/49/labels{/name}","comments_url":"https://api.github.com/repos/seandavi/GEOquery/issues/49/comments","events_url":"https://api.github.com/repos/seandavi/GEOquery/issues/49/events","html_url":"https://github.com/seandavi/GEOquery/issues/49","id":272754202,"node_id":"MDU6SXNzdWUyNzI3NTQyMDI=","number":49,"title":"getGEO fails on some GSEs","user":{"login":"seandavi","id":92435,"node_id":"MDQ6VXNlcjkyNDM1","avatar_url":"https://avatars1.githubusercontent.com/u/92435?v=4","gravatar_id":"","url":"https://api.github.com/users/seandavi","html_url":"https://github.com/seandavi","followers_url":"https://api.github.com/users/seandavi/followers","following_url":"https://api.github.com/users/seandavi/following{/other_user}","gists_url":"https://api.github.com/users/seandavi/gists{/gist_id}","starred_url":"https://api.github.com/users/seandavi/starred{/owner}{/repo}","subscriptions_url":"https://api.github.com/users/seandavi/subscriptions","organizations_url":"https://api.github.com/users/seandavi/orgs","repos_url":"https://api.github.com/users/seandavi/repos","events_url":"https://api.github.com/users/seandavi/events{/privacy}","received_events_url":"https://api.github.com/users/seandavi/received_events","type":"User","site_admin":false},"labels":[{"id":48490821,"node_id":"MDU6TGFiZWw0ODQ5MDgyMQ==","url":"https://api.github.com/repos/seandavi/GEOquery/labels/bug","name":"bug","color":"fc2929","default":true}],"state":"closed","locked":false,"assignee":{"login":"seandavi","id":92435,"node_id":"MDQ6VXNlcjkyNDM1","avatar_url":"https://avatars1.githubusercontent.com/u/92435?v=4","gravatar_id":"","url":"https://api.github.com/users/seandavi","html_url":"https://github.com/seandavi","followers_url":"https://api.github.com/users/seandavi/followers","following_url":"https://api.github.com/users/seandavi/following{/other_user}","gists_url":"https://api.github.com/users/seandavi/gists{/gist_id}","starred_url":"https://api.github.com/users/seandavi/starred{/owner}{/repo}","subscriptions_url":"https://api.github.com/users/seandavi/subscriptions","organizations_url":"https://api.github.com/users/seandavi/orgs","repos_url":"https://api.github.com/users/seandavi/repos","events_url":"https://api.github.com/users/seandavi/events{/privacy}","received_events_url":"https://api.github.com/users/seandavi/received_events","type":"User","site_admin":false},"assignees":[{"login":"seandavi","id":92435,"node_id":"MDQ6VXNlcjkyNDM1","avatar_url":"https://avatars1.githubusercontent.com/u/92435?v=4","gravatar_id":"","url":"https://api.github.com/users/seandavi","html_url":"https://github.com/seandavi","followers_url":"https://api.github.com/users/seandavi/followers","following_url":"https://api.github.com/users/seandavi/following{/other_user}","gists_url":"https://api.github.com/users/seandavi/gists{/gist_id}","starred_url":"https://api.github.com/users/seandavi/starred{/owner}{/repo}","subscriptions_url":"https://api.github.com/users/seandavi/subscriptions","organizations_url":"https://api.github.com/users/seandavi/orgs","repos_url":"https://api.github.com/users/seandavi/repos","events_url":"https://api.github.com/users/seandavi/events{/privacy}","received_events_url":"https://api.github.com/users/seandavi/received_events","type":"User","site_admin":false}],"milestone":null,"comments":1,"created_at":"2017-11-09T22:44:22Z","updated_at":"2018-11-07T03:42:07Z","closed_at":"2017-11-15T04:37:39Z","author_association":"OWNER","body":": reported by Alex Abbas via email \r\n\r\n```\r\n> getGEO(\"GSE83452”)\r\nFound 1 file(s)\r\nGSE83452_series_matrix.txt.gz\r\ntrying URL 'https://ftp.ncbi.nlm.nih.gov/geo/series/GSE83nnn/GSE83452/matrix/GSE83452_series_matrix.txt.gz'\r\nContent type 'application/x-gzip' length 40807397 bytes (38.9 MB)\r\n==================================================\r\ndownloaded 38.9 MB\r\n\r\nParsed with column specification:\r\ncols(\r\n  .default = col_double(),\r\n  ID_REF = col_integer()\r\n)\r\nSee spec(...) for full column specifications.\r\n|====================================================================================================================================| 100%   93 MB\r\nFile stored at:\r\n/var/folders/wf/65nq9x_d4xj9ttpbz7shlkgc0000gn/T//RtmpbPhopr/GPL16686.soft\r\nWarning: 190 parsing failures.\r\nrow # A tibble: 5 x 5 col     row   col   expected         actual         file expected   <int> <chr>      <chr>          <chr>        <chr> actual 1 53792    ID an integer AFFX-BioB-3_at literal data file 2 53793    ID an integer AFFX-BioB-3_st literal data row 3 53794    ID an integer AFFX-BioB-5_at literal data col 4 53795    ID an integer AFFX-BioB-5_st literal data expected 5 53796    ID an integer AFFX-BioB-M_at literal data\r\n... ................. ... .................................................... ........ .................................................... ...... .................................................... .... .................................................... ... .................................................... ... .................................................... ........ ....................................................\r\nSee problems(...) for more details.\r\n\r\nError in `row.names<-.data.frame`(`*tmp*`, value = value) :\r\n  duplicate 'row.names' are not allowed\r\nIn addition: Warning messages:\r\n1: attributes are not identical across measure variables;\r\nthey will be dropped\r\n2: In rbind(names(probs), probs_f) :\r\n  number of columns of result is not a multiple of vector length (arg 1)\r\n3: non-unique value when setting 'row.names': ‘NA’\r\n> sessionInfo()\r\nR version 3.4.2 (2017-09-28)\r\nPlatform: x86_64-apple-darwin15.6.0 (64-bit)\r\nRunning under: macOS Sierra 10.12.6\r\n\r\nMatrix products: default\r\nBLAS: /System/Library/Frameworks/Accelerate.framework/Versions/A/Frameworks/vecLib.framework/Versions/A/libBLAS.dylib\r\nLAPACK: /Library/Frameworks/R.framework/Versions/3.4/Resources/lib/libRlapack.dylib\r\n\r\nlocale:\r\n[1] en_US.UTF-8/en_US.UTF-8/en_US.UTF-8/C/en_US.UTF-8/en_US.UTF-8\r\n\r\nattached base packages:\r\n[1] parallel  stats     graphics  grDevices utils     datasets  methods   base\r\n\r\nother attached packages:\r\n[1] GEOquery_2.46.3     bindrcpp_0.2        Biobase_2.38.0      BiocGenerics_0.24.0 ggplot2_2.2.1       tidyr_0.7.2         dplyr_0.7.4\r\n\r\nloaded via a namespace (and not attached):\r\n [1] Rcpp_0.12.13     xml2_1.1.1       bindr_0.1        magrittr_1.5     hms_0.3          tidyselect_0.2.3 munsell_0.4.3    colorspace_1.3-2\r\n [9] R6_2.2.2         rlang_0.1.4      httr_1.3.1       plyr_1.8.4       tools_3.4.2      grid_3.4.2       gtable_0.2.0     lazyeval_0.2.1\r\n[17] assertthat_0.2.0 tibble_1.3.4     readr_1.1.1      purrr_0.2.4      bitops_1.0-6     curl_3.0         RCurl_1.95-4.8   glue_1.2.0\r\n[25] labeling_0.3     stringi_1.1.5    compiler_3.4.2   scales_0.5.0     XML_3.98-1.9     pkgconfig_2.0.1\r\n```"},"comment":{"url":"https://api.github.com/repos/seandavi/GEOquery/issues/comments/436494376","html_url":"https://github.com/seandavi/GEOquery/issues/49#issuecomment-436494376","issue_url":"https://api.github.com/repos/seandavi/GEOquery/issues/49","id":436494376,"node_id":"MDEyOklzc3VlQ29tbWVudDQzNjQ5NDM3Ng==","user":{"login":"seandavi","id":92435,"node_id":"MDQ6VXNlcjkyNDM1","avatar_url":"https://avatars1.githubusercontent.com/u/92435?v=4","gravatar_id":"","url":"https://api.github.com/users/seandavi","html_url":"https://github.com/seandavi","followers_url":"https://api.github.com/users/seandavi/followers","following_url":"https://api.github.com/users/seandavi/following{/other_user}","gists_url":"https://api.github.com/users/seandavi/gists{/gist_id}","starred_url":"https://api.github.com/users/seandavi/starred{/owner}{/repo}","subscriptions_url":"https://api.github.com/users/seandavi/subscriptions","organizations_url":"https://api.github.com/users/seandavi/orgs","repos_url":"https://api.github.com/users/seandavi/repos","events_url":"https://api.github.com/users/seandavi/events{/privacy}","received_events_url":"https://api.github.com/users/seandavi/received_events","type":"User","site_admin":false},"created_at":"2018-11-07T03:42:07Z","updated_at":"2018-11-07T03:42:07Z","author_association":"OWNER","body":"Updating R and Bioconductor will likely do the trick."}}
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