Reasoning for illegal operation
0
0
Entering edit mode
lisa8191 • 0
@lisa8191-14639
Last seen 6.9 years ago

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"))

tcgabiolinks illegaloperation gdcprepare • 977 views
ADD COMMENT

Login before adding your answer.

Traffic: 596 users visited in the last hour
Help About
FAQ
Access RSS
API
Stats

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.

Powered by the version 2.3.6