Open CianMurphy opened 10 months ago
Since the weekend I have noticed this GDC prepare step does not work
eg if following https://bioconductor.org/packages/devel/bioc/vignettes/TCGAbiolinks/inst/doc/analysis.html
I get the error:
> BRCA.Rnaseq.SE <- GDCprepare(query) |==============================================================================================================================================================================================================================|100% Completed after 0 s Starting to add information to samples => Add clinical information to samples => Adding TCGA molecular information from marker papers => Information will have prefix 'paper_' brca subtype information from:doi.org/10.1016/j.ccell.2018.03.014 Error in load(zfile, envir = tmp_env) : empty (zero-byte) input file > sessionInfo() R version 4.2.0 (2022-04-22) Platform: x86_64-pc-linux-gnu (64-bit) Running under: CentOS Linux 7 (Core) Matrix products: default BLAS/LAPACK: /flask/apps/eb/software/FlexiBLAS/3.0.4-GCC-11.2.0/lib64/libflexiblas.so.3.0 locale: [1] LC_CTYPE=en_GB.UTF-8 LC_NUMERIC=C LC_TIME=en_GB.UTF-8 LC_COLLATE=en_GB.UTF-8 LC_MONETARY=en_GB.UTF-8 LC_MESSAGES=en_GB.UTF-8 LC_PAPER=en_GB.UTF-8 LC_NAME=C LC_ADDRESS=C [10] LC_TELEPHONE=C LC_MEASUREMENT=en_GB.UTF-8 LC_IDENTIFICATION=C attached base packages: [1] stats graphics grDevices utils datasets methods base other attached packages: [1] TCGAbiolinks_2.25.3 loaded via a namespace (and not attached): [1] MatrixGenerics_1.10.0 Biobase_2.58.0 httr_1.4.7 tidyr_1.3.0 bit64_4.0.5 jsonlite_1.8.7 R.utils_2.12.2 BiocManager_1.30.22 [9] stats4_4.2.0 BiocFileCache_2.6.1 blob_1.2.4 GenomeInfoDbData_1.2.9 progress_1.2.2 pillar_1.9.0 RSQLite_2.3.1 lattice_0.20-45 [17] glue_1.6.2 downloader_0.4 digest_0.6.29 GenomicRanges_1.50.2 XVector_0.38.0 rvest_1.0.3 colorspace_2.0-3 Matrix_1.6-1 [25] R.oo_1.25.0 plyr_1.8.8 XML_3.99-0.14 pkgconfig_2.0.3 biomaRt_2.54.1 zlibbioc_1.44.0 purrr_1.0.2 scales_1.2.1 [33] tzdb_0.4.0 tibble_3.2.1 KEGGREST_1.38.0 generics_0.1.3 TCGAbiolinksGUI.data_1.18.0 IRanges_2.32.0 ggplot2_3.4.3 cachem_1.0.8 [41] withr_2.5.0 SummarizedExperiment_1.28.0 BiocGenerics_0.44.0 cli_3.6.1 magrittr_2.0.3 crayon_1.5.1 memoise_2.0.1 R.methodsS3_1.8.2 [49] fansi_1.0.3 xml2_1.3.3 tools_4.2.0 data.table_1.14.8 prettyunits_1.1.1 hms_1.1.3 lifecycle_1.0.3 matrixStats_1.0.0 [57] stringr_1.5.0 S4Vectors_0.36.2 munsell_0.5.0 DelayedArray_0.24.0 AnnotationDbi_1.60.2 Biostrings_2.66.0 compiler_4.2.0 GenomeInfoDb_1.34.9 [65] rlang_1.1.1 grid_4.2.0 RCurl_1.98-1.12 rappdirs_0.3.3 bitops_1.0-7 gtable_0.3.1 DBI_1.1.3 curl_5.0.2 [73] R6_2.5.1 knitr_1.43 dplyr_1.1.3 fastmap_1.1.1 bit_4.0.5 utf8_1.2.2 filelock_1.0.2 readr_2.1.4 [81] stringi_1.7.6 Rcpp_1.0.11 vctrs_0.6.3 png_0.1-8 dbplyr_2.3.3 tidyselect_1.2.0 xfun_0.40 >
Since the weekend I have noticed this GDC prepare step does not work
eg if following https://bioconductor.org/packages/devel/bioc/vignettes/TCGAbiolinks/inst/doc/analysis.html
I get the error: