When downloading the TCGA via GDCprepare, I kept getting the below error. Wondering if it's something conflicting with my computer?
The full code I ran:
tcga.proj <- "TCGA-BRCA" exp.proj <- GDCquery(project = tcga.proj, data.category = "Transcriptome Profiling", data.type = "Gene Expression Quantification", sample.type = c("Primary solid Tumor","Metastatic"), workflow.type = "HTSeq - FPKM") GDCdownload(exp.proj) exp.dat <- GDCprepare(query = exp.proj, save = TRUE, save.filename = paste0(tcga.proj,"_exp.rda"))
sessionInfo():
R version 3.3.3 (2017-03-06) Platform: x86_64-pc-linux-gnu (64-bit) Running under: CentOS release 6.9 (Final) locale: [1] LC_CTYPE=en_US.UTF-8 LC_NUMERIC=C LC_TIME=en_US.UTF-8 LC_COLLATE=en_US.UTF-8 LC_MONETARY=en_US.UTF-8 [6] LC_MESSAGES=en_US.UTF-8 LC_PAPER=en_US.UTF-8 LC_NAME=C LC_ADDRESS=C LC_TELEPHONE=C [11] LC_MEASUREMENT=en_US.UTF-8 LC_IDENTIFICATION=C attached base packages: [1] parallel stats4 stats graphics grDevices utils datasets methods base other attached packages: [1] doMC_1.3.5 iterators_1.0.9 foreach_1.4.4 pec_2.5.4 prodlim_1.6.1 [6] rms_5.1-1 SparseM_1.77 Hmisc_4.0-3 Formula_1.2-2 survival_2.41-3 [11] lattice_0.20-35 BiocParallel_1.8.2 MASS_7.3-47 ggplot2_2.2.1 RColorBrewer_1.1-2 [16] pheatmap_1.0.8 reshape2_1.4.3 plyr_1.8.4 DT_0.2 dplyr_0.7.4 [21] SummarizedExperiment_1.4.0 Biobase_2.34.0 GenomicRanges_1.26.4 GenomeInfoDb_1.10.3 IRanges_2.8.2 [26] S4Vectors_0.12.2 BiocGenerics_0.20.0 TCGAbiolinks_2.7.3 BiocInstaller_1.24.0 vimcom_1.0-0 [31] setwidth_1.0-4 colorout_1.0-3 loaded via a namespace (and not attached): [1] backports_1.1.2 circlize_0.4.2 aroma.light_3.4.0 selectr_0.3-1 ConsensusClusterPlus_1.38.0 [6] lazyeval_0.2.1 splines_3.3.3 TH.data_1.0-8 digest_0.6.12 htmltools_0.3.6 [11] viridis_0.4.0 checkmate_1.8.5 magrittr_1.5 memoise_1.1.0 cluster_2.0.6 [16] doParallel_1.0.11 limma_3.30.13 ComplexHeatmap_1.12.0 Biostrings_2.42.1 readr_1.1.1 [21] annotate_1.52.1 matrixStats_0.52.2 R.utils_2.6.0 sandwich_2.4-0 colorspace_1.3-2 [26] blob_1.1.0 rvest_0.3.2 ggrepel_0.7.0 RCurl_1.95-4.8 jsonlite_1.5 [31] genefilter_1.56.0 bindr_0.1 zoo_1.8-0 glue_1.2.0 survminer_0.4.1 [36] gtable_0.2.0 zlibbioc_1.20.0 XVector_0.14.1 MatrixModels_0.4-1 GetoptLong_0.1.6 [41] kernlab_0.9-25 shape_1.4.3 prabclus_2.2-6 DEoptimR_1.0-8 scales_0.5.0 [46] DESeq_1.26.0 mvtnorm_1.0-6 DBI_0.7 edgeR_3.16.5 ggthemes_3.4.0 [51] Rcpp_0.12.14 htmlTable_1.11.0 viridisLite_0.2.0 xtable_1.8-2 cmprsk_2.2-7 [56] foreign_0.8-69 bit_1.1-12 matlab_1.0.2 mclust_5.4 km.ci_0.5-2 [61] lava_1.5.1 htmlwidgets_0.9 httr_1.3.1 fpc_2.1-10 acepack_1.4.1 [66] modeltools_0.2-21 pkgconfig_2.0.1 XML_3.98-1.9 R.methodsS3_1.7.1 flexmix_2.3-14 [71] nnet_7.3-12 locfit_1.5-9.1 rlang_0.1.4 AnnotationDbi_1.36.2 munsell_0.4.3 [76] tools_3.3.3 downloader_0.4 RSQLite_2.0 broom_0.4.3 stringr_1.2.0 [81] knitr_1.17 bit64_0.9-7 timereg_1.9.1 robustbase_0.92-8 survMisc_0.5.4 [86] purrr_0.2.4 dendextend_1.6.0 bindrcpp_0.2 EDASeq_2.8.0 nlme_3.1-131
Error messages:
*** caught illegal operation ***
address 0x7ff11205cf85, cause 'illegal operand'
Traceback:
1: .Call("readr_read_connection_", PACKAGE = "readr", con, chunk_size)
2: read_connection_(con)
3: read_connection(file)
4: read_delimited(file, tokenizer, col_names = col_names, col_types = col_types, locale = locale, skip = skip, comment = comment, n_max = n_max, guess_max = guess_max, progress = progress)
5: read_tsv(file = files[i], col_names = FALSE, col_types = cols(X1 = col_character(), X2 = col_double()))
6: readTranscriptomeProfiling(files = files, data.type = ifelse(!is.na(query$data.type), as.character(query$data.type), unique(query$results[[1]]$data_type)), workflow.type = unique(query$results[[1]]$analysis_workflow_type), cases = query$results[[1]]$cases, summarizedExperiment)
7: GDCprepare(query = exp.proj, save = TRUE, save.filename = paste0(tcga.proj, "_exp.rda"))