Question: Reasoning for illegal operation
0
gravatar for lisa8191
16 months ago by
lisa81910
lisa81910 wrote:

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"))

ADD COMMENTlink modified 16 months ago • written 16 months ago by lisa81910
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