{"action":"closed","issue":{"url":"https://api.github.com/repos/BioinformaticsFMRP/TCGAbiolinks/issues/231","repository_url":"https://api.github.com/repos/BioinformaticsFMRP/TCGAbiolinks","labels_url":"https://api.github.com/repos/BioinformaticsFMRP/TCGAbiolinks/issues/231/labels{/name}","comments_url":"https://api.github.com/repos/BioinformaticsFMRP/TCGAbiolinks/issues/231/comments","events_url":"https://api.github.com/repos/BioinformaticsFMRP/TCGAbiolinks/issues/231/events","html_url":"https://github.com/BioinformaticsFMRP/TCGAbiolinks/issues/231","id":333828177,"node_id":"MDU6SXNzdWUzMzM4MjgxNzc=","number":231,"title":"Error with GDCdownload on Windows","user":{"login":"abg28","id":40406627,"node_id":"MDQ6VXNlcjQwNDA2NjI3","avatar_url":"https://avatars3.githubusercontent.com/u/40406627?v=4","gravatar_id":"","url":"https://api.github.com/users/abg28","html_url":"https://github.com/abg28","followers_url":"https://api.github.com/users/abg28/followers","following_url":"https://api.github.com/users/abg28/following{/other_user}","gists_url":"https://api.github.com/users/abg28/gists{/gist_id}","starred_url":"https://api.github.com/users/abg28/starred{/owner}{/repo}","subscriptions_url":"https://api.github.com/users/abg28/subscriptions","organizations_url":"https://api.github.com/users/abg28/orgs","repos_url":"https://api.github.com/users/abg28/repos","events_url":"https://api.github.com/users/abg28/events{/privacy}","received_events_url":"https://api.github.com/users/abg28/received_events","type":"User","site_admin":false},"labels":[],"state":"closed","locked":false,"assignee":null,"assignees":[],"milestone":null,"comments":2,"created_at":"2018-06-19T20:33:16Z","updated_at":"2018-06-20T16:26:54Z","closed_at":"2018-06-20T16:26:54Z","author_association":"NONE","body":"Hello,\r\n\r\nI am attempting to use the GDCdownload function with method set to \"client\", but when I run my code I receive the following error:\r\n\r\n```\r\n> GDCdownload(normalQuery, method = \"client\")\r\nDownloading data for project TCGA-LUAD\r\ntrying URL 'https://gdc.nci.nih.gov/files/public/file/gdc-client_v1.3.0_Windows_x64.zip.zip'\r\nError in download.file(url, method = method, ...) : \r\n  cannot open URL 'https://gdc.nci.nih.gov/files/public/file/gdc-client_v1.3.0_Windows_x64.zip.zip'\r\n```\r\n\r\nI think the error might be caused by the extra \".zip\" in the URL, since when I run my script on my Mac everything seems to work ok (unfortunately I need to get this working on a Windows computer as well).  I would greatly appreciate your insight!  And a huge thank you for making this toolset!\r\n\r\nBest,\r\nAlex\r\n\r\n\r\nFor reference, here is my session info:\r\n\r\n> sessionInfo()\r\nR version 3.5.0 (2018-04-23)\r\nPlatform: x86_64-w64-mingw32/x64 (64-bit)\r\nRunning under: Windows >= 8 x64 (build 9200)\r\n\r\nMatrix products: default\r\n\r\nlocale:\r\n[1] LC_COLLATE=English_United States.1252  LC_CTYPE=English_United States.1252    LC_MONETARY=English_United States.1252\r\n[4] LC_NUMERIC=C                           LC_TIME=English_United States.1252    \r\n\r\nattached base packages:\r\n[1] parallel  stats4    stats     graphics  grDevices utils     datasets  methods   base     \r\n\r\nother attached packages:\r\n [1] TCGAbiolinks_2.9.1          SummarizedExperiment_1.10.1 DelayedArray_0.6.1          BiocParallel_1.14.1        \r\n [5] matrixStats_0.53.1          Biobase_2.40.0              GenomicRanges_1.32.3        GenomeInfoDb_1.16.0        \r\n [9] IRanges_2.14.10             S4Vectors_0.18.3            BiocGenerics_0.26.0         DT_0.4                     \r\n[13] dplyr_0.7.5                 BiocInstaller_1.30.0       \r\n\r\nloaded via a namespace (and not attached):\r\n  [1] circlize_0.4.4              aroma.light_3.10.0          plyr_1.8.4                  selectr_0.4-1              \r\n  [5] ConsensusClusterPlus_1.44.0 lazyeval_0.2.1              splines_3.5.0               ggplot2_2.2.1              \r\n  [9] sva_3.28.0                  digest_0.6.15               foreach_1.4.4               htmltools_0.3.6            \r\n [13] magrittr_1.5                memoise_1.1.0               cluster_2.0.7-1             doParallel_1.0.11          \r\n [17] limma_3.36.1                ComplexHeatmap_1.18.0       Biostrings_2.48.0           readr_1.1.1                \r\n [21] annotate_1.58.0             R.utils_2.6.0               prettyunits_1.0.2           colorspace_1.3-2           \r\n [25] blob_1.1.1                  rvest_0.3.2                 ggrepel_0.8.0               crayon_1.3.4               \r\n [29] RCurl_1.95-4.10             jsonlite_1.5                genefilter_1.62.0           bindr_0.1.1                \r\n [33] survival_2.41-3             zoo_1.8-2                   iterators_1.0.9             glue_1.2.0                 \r\n [37] survminer_0.4.2             gtable_0.2.0                zlibbioc_1.26.0             XVector_0.20.0             \r\n [41] GetoptLong_0.1.7            shape_1.4.4                 scales_0.5.0                DESeq_1.32.0               \r\n [45] DBI_1.0.0                   edgeR_3.22.2                ggthemes_3.5.0              Rcpp_0.12.17               \r\n [49] xtable_1.8-2                progress_1.2.0              cmprsk_2.2-7                foreign_0.8-70             \r\n [53] bit_1.1-14                  matlab_1.0.2                km.ci_0.5-2                 htmlwidgets_1.2            \r\n [57] httr_1.3.1                  RColorBrewer_1.1-2          pkgconfig_2.0.1             XML_3.98-1.11              \r\n [61] R.methodsS3_1.7.1           locfit_1.5-9.1              tidyselect_0.2.4            rlang_0.2.1                \r\n [65] reshape2_1.4.3              AnnotationDbi_1.42.1        munsell_0.5.0               tools_3.5.0                \r\n [69] downloader_0.4              RSQLite_2.1.1               devtools_1.13.5             broom_0.4.4                \r\n [73] stringr_1.3.1               knitr_1.20                  bit64_0.9-7                 survMisc_0.5.4             \r\n [77] purrr_0.2.5                 bindrcpp_0.2.2              EDASeq_2.14.0               nlme_3.1-137               \r\n [81] R.oo_1.22.0                 xml2_1.2.0                  biomaRt_2.36.1              compiler_3.5.0             \r\n [85] curl_3.2                    tibble_1.4.2                geneplotter_1.58.0          stringi_1.1.7              \r\n [89] GenomicFeatures_1.32.0      lattice_0.20-35             Matrix_1.2-14               psych_1.8.4                \r\n [93] KMsurv_0.1-5                pillar_1.2.3                GlobalOptions_0.1.0         data.table_1.11.4          \r\n [97] bitops_1.0-6                rtracklayer_1.40.3          R6_2.2.2                    latticeExtra_0.6-28        \r\n[101] hwriter_1.3.2               ShortRead_1.38.0            gridExtra_2.3               codetools_0.2-15           \r\n[105] assertthat_0.2.0            rjson_0.2.20                withr_2.1.2                 GenomicAlignments_1.16.0   \r\n[109] Rsamtools_1.32.0            mnormt_1.5-5                GenomeInfoDbData_1.1.0      mgcv_1.8-23                \r\n[113] hms_0.4.2                   grid_3.5.0                  tidyr_0.8.1                 git2r_0.21.0               \r\n[117] ggpubr_0.1.6   \r\n"}}
{"actor":{"display_login":"abg28"}}