{"action":"opened","issue":{"url":"https://api.github.com/repos/BioinformaticsFMRP/TCGAbiolinks/issues/221","repository_url":"https://api.github.com/repos/BioinformaticsFMRP/TCGAbiolinks","labels_url":"https://api.github.com/repos/BioinformaticsFMRP/TCGAbiolinks/issues/221/labels{/name}","comments_url":"https://api.github.com/repos/BioinformaticsFMRP/TCGAbiolinks/issues/221/comments","events_url":"https://api.github.com/repos/BioinformaticsFMRP/TCGAbiolinks/issues/221/events","html_url":"https://github.com/BioinformaticsFMRP/TCGAbiolinks/issues/221","id":327758020,"number":221,"title":"GDCdownload fails with \"tar: unrecognized archive format\"","user":{"login":"bnostendorf","id":22296218,"avatar_url":"https://avatars2.githubusercontent.com/u/22296218?v=4","gravatar_id":"","url":"https://api.github.com/users/bnostendorf","html_url":"https://github.com/bnostendorf","followers_url":"https://api.github.com/users/bnostendorf/followers","following_url":"https://api.github.com/users/bnostendorf/following{/other_user}","gists_url":"https://api.github.com/users/bnostendorf/gists{/gist_id}","starred_url":"https://api.github.com/users/bnostendorf/starred{/owner}{/repo}","subscriptions_url":"https://api.github.com/users/bnostendorf/subscriptions","organizations_url":"https://api.github.com/users/bnostendorf/orgs","repos_url":"https://api.github.com/users/bnostendorf/repos","events_url":"https://api.github.com/users/bnostendorf/events{/privacy}","received_events_url":"https://api.github.com/users/bnostendorf/received_events","type":"User","site_admin":false},"labels":[],"state":"open","locked":false,"assignee":null,"assignees":[],"milestone":null,"comments":0,"created_at":"2018-05-30T14:30:35Z","updated_at":"2018-05-30T14:30:35Z","closed_at":null,"author_association":"NONE","body":"Hi Tiago, \r\nmy previously working script to download RNAseq expression data from GDC fails with the error message \"`tar: unrecognized archive format`\". I tried downloading with `method` set to `client`, but in this case the download stalls at a random point without giving an error. Can you reproduce this error or is it something on my end? \r\nThank you!\r\nBenjamin \r\n\r\n-----------\r\n```\r\nlibrary(TCGAbiolinks)\r\nproject_name <- \"TCGA-BRCA\"\r\n  query <- GDCquery(\r\n    project = project_name,\r\n    data.category = \"Gene expression\",\r\n    data.type = \"Gene expression quantification\",\r\n    platform = \"Illumina HiSeq\",\r\n    experimental.strategy = \"RNA-Seq\",\r\n    sample.type = c(\"Primary solid Tumor\"), \r\n    file.type = \"results\",\r\n    legacy = TRUE\r\n    )\r\n\r\n  GDCdownload(query,\r\n              directory = \"data/expression_data\")\r\n\r\ndata <- \r\n  GDCprepare(query,\r\n             save = TRUE,\r\n             save.filename = NGS_raw,\r\n             remove.files.prepared = FALSE, \r\n             directory = \"data/expression_data\"\r\n             )\r\n```\r\n-----------\r\n`sessionInfo()`\r\nR version 3.5.0 (2018-04-23)\r\nPlatform: x86_64-apple-darwin15.6.0 (64-bit)\r\nRunning under: macOS High Sierra 10.13.4\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/3.5/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] stats     graphics  grDevices utils     datasets  methods   base     \r\n\r\nother attached packages:\r\n[1] TCGAbiolinks_2.8.0\r\n\r\nloaded via a namespace (and not attached):\r\n  [1] colorspace_1.3-2            selectr_0.4-1               rjson_0.2.19               \r\n  [4] hwriter_1.3.2               circlize_0.4.3              XVector_0.20.0             \r\n  [7] GenomicRanges_1.32.3        GlobalOptions_0.0.13        ggpubr_0.1.6               \r\n [10] matlab_1.0.2                ggrepel_0.8.0               bit64_0.9-7                \r\n [13] AnnotationDbi_1.42.1        xml2_1.2.0                  codetools_0.2-15           \r\n [16] splines_3.5.0               R.methodsS3_1.7.1           mnormt_1.5-5               \r\n [19] doParallel_1.0.11           DESeq_1.32.0                geneplotter_1.58.0         \r\n [22] knitr_1.20                  jsonlite_1.5                Rsamtools_1.32.0           \r\n [25] km.ci_0.5-2                 broom_0.4.4                 annotate_1.58.0            \r\n [28] cluster_2.0.7-1             R.oo_1.22.0                 readr_1.1.1                \r\n [31] compiler_3.5.0              httr_1.3.1                  assertthat_0.2.0           \r\n [34] Matrix_1.2-14               lazyeval_0.2.1              limma_3.36.1               \r\n [37] prettyunits_1.0.2           tools_3.5.0                 bindrcpp_0.2.2             \r\n [40] gtable_0.2.0                glue_1.2.0                  GenomeInfoDbData_1.1.0     \r\n [43] reshape2_1.4.3              dplyr_0.7.5                 ggthemes_3.5.0             \r\n [46] ShortRead_1.38.0            Rcpp_0.12.17                Biobase_2.40.0             \r\n [49] Biostrings_2.48.0           nlme_3.1-137                rtracklayer_1.40.2         \r\n [52] iterators_1.0.9             psych_1.8.4                 stringr_1.3.1              \r\n [55] rvest_0.3.2                 XML_3.98-1.11               edgeR_3.22.1               \r\n [58] zoo_1.8-1                   zlibbioc_1.26.0             scales_0.5.0               \r\n [61] aroma.light_3.10.0          hms_0.4.2                   parallel_3.5.0             \r\n [64] SummarizedExperiment_1.10.1 RColorBrewer_1.1-2          curl_3.2                   \r\n [67] ComplexHeatmap_1.18.0       yaml_2.1.19                 memoise_1.1.0              \r\n [70] gridExtra_2.3               KMsurv_0.1-5                ggplot2_2.2.1              \r\n [73] downloader_0.4              biomaRt_2.36.0              latticeExtra_0.6-28        \r\n [76] stringi_1.2.2               RSQLite_2.1.1               genefilter_1.62.0          \r\n [79] S4Vectors_0.18.2            foreach_1.4.4               GenomicFeatures_1.32.0     \r\n [82] BiocGenerics_0.26.0         BiocParallel_1.14.1         shape_1.4.4                \r\n [85] GenomeInfoDb_1.16.0         rlang_0.2.0                 pkgconfig_2.0.1            \r\n [88] matrixStats_0.53.1          bitops_1.0-6                lattice_0.20-35            \r\n [91] purrr_0.2.4                 bindr_0.1.1                 GenomicAlignments_1.16.0   \r\n [94] cmprsk_2.2-7                bit_1.1-13                  tidyselect_0.2.4           \r\n [97] plyr_1.8.4                  magrittr_1.5                R6_2.2.2                   \r\n[100] IRanges_2.14.10             DelayedArray_0.6.0          DBI_1.0.0                  \r\n[103] mgcv_1.8-23                 pillar_1.2.2                foreign_0.8-70             \r\n[106] survival_2.42-3             RCurl_1.95-4.10             tibble_1.4.2               \r\n[109] EDASeq_2.14.0               survMisc_0.5.4              GetoptLong_0.1.6           \r\n[112] progress_1.1.2              locfit_1.5-9.1              grid_3.5.0                 \r\n[115] sva_3.28.0                  data.table_1.11.2           blob_1.1.1                 \r\n[118] ConsensusClusterPlus_1.44.0 digest_0.6.15               xtable_1.8-2               \r\n[121] tidyr_0.8.1                 R.utils_2.6.0               stats4_3.5.0               \r\n[124] munsell_0.4.3               survminer_0.4.2   "}}
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