TCGAbiolinks not working anymore
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Entering edit mode
10 months ago

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
R TCGAbiolinks GDC • 353 views
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