Entering edit mode
11 weeks ago
master chief
•
0
The script in this tutorial does not work anymore
https://bioconductor.org/packages/devel/bioc/vignettes/TCGAbiolinks/inst/doc/analysis.html
I get to GDCprepare stage and get error:
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 `
Starting to add information to samples
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] optparse_1.7.3 data.table_1.14.8 ggrepel_0.9.3 easyPubMed_2.13 limma_3.54.2 lubridate_1.9.2 forcats_1.0.0 stringr_1.5.0 purrr_1.0.2 readr_2.1.4 tidyr_1.3.0 tibble_3.2.1
[13] ggplot2_3.4.3 tidyverse_2.0.0 biomaRt_2.54.1 dplyr_1.1.3 TCGAbiolinks_2.25.3
loaded via a namespace (and not attached):
[1] MatrixGenerics_1.10.0 Biobase_2.58.0 httr_1.4.7 vroom_1.6.3 bit64_4.0.5 jsonlite_1.8.7 R.utils_2.12.2 stats4_4.2.0
[9] 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 glue_1.6.2
[17] downloader_0.4 digest_0.6.29 GenomicRanges_1.50.2 XVector_0.38.0 rvest_1.0.3 colorspace_2.0-3 R.oo_1.25.0 Matrix_1.6-1
[25] plyr_1.8.8 XML_3.99-0.14 pkgconfig_2.0.3 zlibbioc_1.44.0 scales_1.2.1 getopt_1.20.3 tzdb_0.4.0 timechange_0.2.0
[33] KEGGREST_1.38.0 generics_0.1.3 TCGAbiolinksGUI.data_1.18.0 IRanges_2.32.0 cachem_1.0.8 withr_2.5.0 SummarizedExperiment_1.28.0 BiocGenerics_0.44.0
[41] cli_3.6.1 magrittr_2.0.3 crayon_1.5.1 memoise_2.0.1 R.methodsS3_1.8.2 fansi_1.0.3 xml2_1.3.3 tools_4.2.0
[49] prettyunits_1.1.1 hms_1.1.3 lifecycle_1.0.3 matrixStats_1.0.0 S4Vectors_0.36.2 munsell_0.5.0 DelayedArray_0.24.0 AnnotationDbi_1.60.2
[57] Biostrings_2.66.0 compiler_4.2.0 GenomeInfoDb_1.34.9 rlang_1.1.1 grid_4.2.0 RCurl_1.98-1.12 rappdirs_0.3.3 bitops_1.0-7
[65] gtable_0.3.1 DBI_1.1.3 curl_5.0.2 R6_2.5.1 knitr_1.43 fastmap_1.1.1 bit_4.0.5 utf8_1.2.2
[73] filelock_1.0.2 stringi_1.7.6 parallel_4.2.0 Rcpp_1.0.11 vctrs_0.6.3 png_0.1-8 dbplyr_2.3.3 tidyselect_1.2.0
[81] xfun_0.40