Hi, I am trying to use GDCdownload (package TCGAbiolinks) but I am having an error all the time when I try to download my data. I do the query and when I try to download it starts downloading for a while and then stops with a error message. I have tried to do it with other query (even from Bioconductor webpage) and I obtain the same message.
The code is obtained from the paper titled "TCGA Workflow: Analyze cancer genomics and epigenomics data using Bioconductor packages" (Silva).
I paste my code and the messages that I am obtaining:
> query.met.gbm=GDCquery(project="TCGA-GBM", legacy=TRUE, data.category="DNA methylation", platform="Illumina Human Methylation 450", barcode=c("TCGA-76-4926-01B-01D-1481-05", "TCGA-28-5211-01C-11D-1844-05")) -------------------------------------- o GDCquery: Searching in GDC database -------------------------------------- Genome of reference: hg19 -------------------------------------------- oo Accessing GDC. This might take a while... -------------------------------------------- [1] "https://api.gdc.cancer.gov/legacy/files/?pretty=true&expand=cases.samples.portions.analytes.aliquots,cases.project,center,analysis,cases.samples&size=988&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-GBM%22]%7D%7D,%7B%22op%22:%22in%22,%22content%22:%7B%22field%22:%22files.data_category%22,%22value%22:[%22DNA%20methylation%22]%7D%7D,%7B%22op%22:%22in%22,%22content%22:%7B%22field%22:%22files.platform%22,%22value%22:[%22Illumina%20Human%20Methylation%20450%22]%7D%7D]%7D&format=JSON" ooo Project: TCGA-GBM -------------------- oo Filtering results -------------------- ooo By platform ooo By barcode ---------------- oo Checking data ---------------- ooo Check if there are duplicated cases ooo Check if there results for the query ------------------- o Preparing output ------------------- > GDCdownload(query.met.gbm) Downloading data for project TCGA-GBM GDCdownload will download 2 files. A total of 42.603084 MB Downloading as: Tue_Dec_18_11_13_35_2018.tar.gz Downloading: 20 MB <simpleWarning in file.create(to[okay]): cannot create file 'GDCdata/TCGA-GBM/legacy/DNA_methylation/Methylation_beta_value/0faddb5f-fe60-4269-90cd-736048a5b061/jhu-usc.edu_GBM.HumanMethylation450.6.lvl-3.TCGA-76-4926-01B-01D-1481-05.txt', reason 'No such file or directory'> <simpleWarning in file.create(to[okay]): cannot create file 'GDCdata/TCGA-GBM/legacy/DNA_methylation/Methylation_beta_value/abb0c4c1-9249-4582-8fa3-34c0a5e3b8e6/jhu-usc.edu_GBM.HumanMethylation450.8.lvl-3.TCGA-28-5211-01C-11D-1844-05.txt', reason 'No such file or directory'> > sessionInfo() R version 3.5.1 (2018-07-02) Platform: x86_64-w64-mingw32/x64 (64-bit) Running under: Windows >= 8 x64 (build 9200) Matrix products: default locale: [1] LC_COLLATE=Spanish_Spain.1252 LC_CTYPE=Spanish_Spain.1252 LC_MONETARY=Spanish_Spain.1252 LC_NUMERIC=C LC_TIME=Spanish_Spain.1252 attached base packages: [1] stats graphics grDevices utils datasets methods base other attached packages: [1] TCGAbiolinks_2.10.0 loaded via a namespace (and not attached): [1] colorspace_1.3-2 selectr_0.4-1 rjson_0.2.20 hwriter_1.3.2 circlize_0.4.5 XVector_0.22.0 [7] GenomicRanges_1.34.0 GlobalOptions_0.1.0 ggpubr_0.2 matlab_1.0.2 ggrepel_0.8.0 bit64_0.9-7 [13] AnnotationDbi_1.44.0 xml2_1.2.0 codetools_0.2-15 splines_3.5.1 R.methodsS3_1.7.1 doParallel_1.0.14 [19] DESeq_1.34.0 geneplotter_1.60.0 knitr_1.21 jsonlite_1.6 Rsamtools_1.34.0 km.ci_0.5-2 [25] broom_0.5.1 annotate_1.60.0 cluster_2.0.7-1 R.oo_1.22.0 readr_1.3.0 compiler_3.5.1 [31] httr_1.4.0 backports_1.1.3 assertthat_0.2.0 Matrix_1.2-14 lazyeval_0.2.1 limma_3.38.3 [37] prettyunits_1.0.2 tools_3.5.1 bindrcpp_0.2.2 gtable_0.2.0 glue_1.3.0 GenomeInfoDbData_1.2.0 [43] dplyr_0.7.8 ggthemes_4.0.1 ShortRead_1.40.0 Rcpp_1.0.0 Biobase_2.42.0 Biostrings_2.50.1 [49] nlme_3.1-137 rtracklayer_1.42.1 iterators_1.0.10 xfun_0.4 stringr_1.3.1 rvest_0.3.2 [55] XML_3.98-1.16 edgeR_3.24.2 zoo_1.8-4 zlibbioc_1.28.0 scales_1.0.0 aroma.light_3.12.0 [61] hms_0.4.2 parallel_3.5.1 SummarizedExperiment_1.12.0 RColorBrewer_1.1-2 curl_3.2 ComplexHeatmap_1.20.0 [67] memoise_1.1.0 gridExtra_2.3 KMsurv_0.1-5 ggplot2_3.1.0 downloader_0.4 biomaRt_2.38.0 [73] latticeExtra_0.6-28 stringi_1.2.4 RSQLite_2.1.1 genefilter_1.64.0 S4Vectors_0.20.1 foreach_1.4.4 [79] GenomicFeatures_1.34.1 BiocGenerics_0.28.0 BiocParallel_1.16.2 shape_1.4.4 GenomeInfoDb_1.18.1 rlang_0.3.0.1 [85] pkgconfig_2.0.2 matrixStats_0.54.0 bitops_1.0-6 lattice_0.20-35 purrr_0.2.5 bindr_0.1.1 [91] cmprsk_2.2-7 GenomicAlignments_1.18.0 bit_1.1-14 tidyselect_0.2.5 plyr_1.8.4 magrittr_1.5 [97] R6_2.3.0 IRanges_2.16.0 generics_0.0.2 DelayedArray_0.8.0 DBI_1.0.0 mgcv_1.8-24 [103] pillar_1.3.1 survival_2.42-3 RCurl_1.95-4.11 tibble_1.4.2 EDASeq_2.16.0 crayon_1.3.4 [109] survMisc_0.5.5 GetoptLong_0.1.7 progress_1.2.0 locfit_1.5-9.1 grid_3.5.1 sva_3.30.0 [115] data.table_1.11.8 blob_1.1.1 ConsensusClusterPlus_1.46.0 digest_0.6.18 xtable_1.8-3 tidyr_0.8.2 [121] R.utils_2.7.0 stats4_3.5.1 munsell_0.5.0 survminer_0.4.3
Huh?
You should consider the full path, not the relative path.
Yes, I saw these and I changed it but I am getting the same result. And anyway with the full path I am getting less than 260 characters so it would not be the problem.
Well, I don't get why, but now it is working. I put it directly on D:\\R and now it works. Thanks!