TCGAbiolinks error

Question

[Elizabeth]

Hello!

I was trying to use TCGAbiolinks as usual in a R-Colab notebook but I got this error:

Bioconductor version 3.17 (BiocManager 1.30.20), R 4.3.0 (2023-04-21)

Installing package(s) 'TCGAbiolinks'

Warning message:
"package 'TCGAbiolinks' is not available for 
Bioconductor version '3.17'

What should I do to fix it?

Thanks!

[ATpoint]

Cannot reproduce. This works: BiocManager::install("TCGAbiolinks"). Please add full command and session info.

[Elizabeth]

Thanks! I am using an R-Colab notebook

sessionInfo()

R version 4.3.0 (2023-04-21) Platform: x86_64-pc-linux-gnu (64-bit) Running under: Ubuntu 20.04.5 LTS

Matrix products: default BLAS: /usr/lib/x86_64-linux-gnu/openblas-pthread/libblas.so.3 LAPACK: /usr/lib/x86_64-linux-gnu/openblas-pthread/liblapack.so.3; LAPACK version 3.9.0

locale: [1] LC_CTYPE=en_US.UTF-8 LC_NUMERIC=C
[3] LC_TIME=en_US.UTF-8 LC_COLLATE=en_US.UTF-8
[5] LC_MONETARY=en_US.UTF-8 LC_MESSAGES=en_US.UTF-8
[7] LC_PAPER=en_US.UTF-8 LC_NAME=C
[9] LC_ADDRESS=C LC_TELEPHONE=C
[11] LC_MEASUREMENT=en_US.UTF-8 LC_IDENTIFICATION=C

time zone: Etc/UTC tzcode source: system (glibc)

attached base packages: [1] stats4 stats graphics grDevices utils datasets methods
[8] base

other attached packages: [1] SummarizedExperiment_1.30.0 Biobase_2.60.0
[3] GenomicRanges_1.52.0 GenomeInfoDb_1.36.0
[5] IRanges_2.34.0 S4Vectors_0.38.0
[7] BiocGenerics_0.46.0 MatrixGenerics_1.12.0
[9] matrixStats_0.63.0

loaded via a namespace (and not attached): [1] crayon_1.5.2 vctrs_0.6.1 cli_3.6.1
[4] rlang_1.1.0 DelayedArray_0.25.0 jsonlite_1.8.3
[7] glue_1.6.2 RCurl_1.98-1.12 htmltools_0.5.5
[10] IRdisplay_1.1 IRkernel_1.3.2 fansi_1.0.4
[13] grid_4.3.0 evaluate_0.20 bitops_1.0-7
[16] fastmap_1.1.1 base64enc_0.1-3 lifecycle_1.0.3
[19] BiocManager_1.30.20 compiler_4.3.0 XVector_0.40.0
[22] lattice_0.21-8 pbdZMQ_0.3-9 digest_0.6.30
[25] repr_1.1.6 utf8_1.2.3 GenomeInfoDbData_1.2.10 [28] pillar_1.9.0 Matrix_1.5-4 uuid_1.1-0
[31] tools_4.3.0 zlibbioc_1.46.0

BiocManager::install("TCGAbiolinks")

'getOption("repos")' replaces Bioconductor standard repositories, see 'help("repositories", package = "BiocManager")' for details. Replacement repositories: CRAN: https://cran.rstudio.com

Bioconductor version 3.17 (BiocManager 1.30.20), R 4.3.0 (2023-04-21)

Installing package(s) 'TCGAbiolinks'

Warning message: “package ‘TCGAbiolinks’ is not available for Bioconductor version '3.17'

A version of this package for your version of R might be available elsewhere, see the ideas at https://cran.r-project.org/doc/manuals/r-patched/R-admin.html#Installing-packages” Old packages: 'bit', 'bslib', 'devtools', 'digest', 'dplyr', 'fontawesome', 'fs', 'gargle', 'gert', 'highr', 'isoband', 'jsonlite', 'pkgload', 'processx', 'ps', 'roxygen2', 'stringr', 'tidyverse', 'tinytex', 'vctrs', 'whisker', 'xfun', 'xml2', 'zip', 'boot', 'foreign', 'MASS'

library(TCGAbiolinks)

Error in library(TCGAbiolinks): there is no package called ‘TCGAbiolinks’ Traceback:

1. library(TCGAbiolinks)

Answer 1

[Mohita]

Try to install it from the GitHub instead from the BioConductor. The link for Installation from GitHub is : https://github.com/BioinformaticsFMRP/TCGAbiolinks.I It worked for me, I hope it will solve your problem.

[Maliha]

Thank you so much. It worked for me now.