if (!requireNamespace("BiocManager", quietly = TRUE))
install.packages("BiocManager")
if (!requireNamespace("cBioPortalData", quietly = TRUE))
BiocManager::install("cBioPortalData")
library(cBioPortalData)
Unfortunately, after loading and installing it finished with the following error after the last prompt libary(cBioPortalData):--
Renée de Leeuw, PhD
Assistant Professor
UIC - Department of Pathology
6095 COMRB
840 S Wood St, Suite 130 CSN, (MC 847)
Chicago, IL, 60612-4325
Phone: (312) 355-4154
E-mail: rdel...@uic.edu
Twitter: @deLeeuwRenee
Pronouns: she/her/hers
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Levi Waldron
Associate Professor
Department of Epidemiology and Biostatistics
CUNY Graduate School of Public Health and Health Policy
Institute for Implementation Science in Population Health
55 W 125th St, New York NY 10035
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Hi,
Thank you for your quick responses. Unfortunately this did not resolve my issue, I still got the same error.
This is the output re: Bioconductor and R versions:
> BiocManager::version()
[1] ‘3.11’
> BiocManager::valid()
[1] TRUE
> BiocManager::install()Bioconductor version 3.11 (BiocManager 1.30.10), R 4.0.0 (2020-04-24)
As for the error and session info, see here:
Error: package or namespace load failed for ‘cBioPortalData’ in loadNamespace(j <- i[[1L]], c(lib.loc, .libPaths()), versionCheck = vI[[j]]):
there is no package called ‘rtracklayer’
>
>
> sessionInfo()
R version 4.0.0 (2020-04-24)
Platform: x86_64-apple-darwin17.0 (64-bit)
Running under: macOS Catalina 10.15.4
Matrix products: default
BLAS: /System/Library/Frameworks/Accelerate.framework/Versions/A/Frameworks/vecLib.framework/Versions/A/libBLAS.dylib
LAPACK: /Library/Frameworks/R.framework/Versions/4.0/Resources/lib/libRlapack.dylib
locale:
[1] en_US.UTF-8/en_US.UTF-8/en_US.UTF-8/C/en_US.UTF-8/en_US.UTF-8
attached base packages:
[1] parallel stats4 stats graphics grDevices utils datasets methods base
other attached packages:
[1] MultiAssayExperiment_1.14.0 SummarizedExperiment_1.18.1 DelayedArray_0.14.0 matrixStats_0.56.0 Biobase_2.48.0 GenomicRanges_1.40.0
[7] GenomeInfoDb_1.24.0 IRanges_2.22.2 S4Vectors_0.26.1 BiocGenerics_0.34.0 AnVIL_1.0.3 dplyr_1.0.0
loaded via a namespace (and not attached):
[1] httr_1.4.1 bit64_0.9-7 jsonlite_1.6.1 splines_4.0.0 assertthat_0.2.1 askpass_1.1
[7] BiocManager_1.30.10 BiocFileCache_1.12.0 blob_1.2.1 GenomeInfoDbData_1.2.3 RTCGAToolbox_2.18.0 progress_1.2.2
[13] yaml_2.2.1 pillar_1.4.4 RSQLite_2.2.0 lattice_0.20-41 glue_1.4.1 limma_3.44.1
[19] digest_0.6.25 XVector_0.28.0 swirl_2.4.5 Matrix_1.2-18 XML_3.99-0.3 pkgconfig_2.0.3
[25] biomaRt_2.44.0 zlibbioc_1.34.0 purrr_0.3.4 RCircos_1.2.1 rapiclient_0.1.3 openssl_1.4.1
[31] tibble_3.0.1 generics_0.0.2 ellipsis_0.3.1 survival_3.1-12 RJSONIO_1.3-1.4 magrittr_1.5
[37] crayon_1.3.4 memoise_1.1.0 xml2_1.3.2 prettyunits_1.1.1 tools_4.0.0 data.table_1.12.8
[43] hms_0.5.3 formatR_1.7 lifecycle_0.2.0 stringr_1.4.0 Biostrings_2.56.0 AnnotationDbi_1.50.0
[49] lambda.r_1.2.4 compiler_4.0.0 rlang_0.4.6 futile.logger_1.4.3 grid_4.0.0 GenomicDataCommons_1.12.0
[55] RCurl_1.98-1.2 rstudioapi_0.11 rappdirs_0.3.1 bitops_1.0-6 testthat_2.3.2 DBI_1.1.0
[61] curl_4.3 R6_2.4.1 bit_1.1-15.2 futile.options_1.0.1 readr_1.3.1 stringi_1.4.6[67] RaggedExperiment_1.12.0 Rcpp_1.0.4.6 vctrs_0.3.0 dbplyr_1.4.4 tidyselect_1.1.0
Hope this helps and thanks for helping me troubleshoot!
Renée
From: mohammed imran Khan <imrankha...@gmail.com>
Sent: Sunday, May 31, 2020 8:37 PM
To: Levi Waldron <lwaldron...@gmail.com>
Cc: JJ Gao <jianji...@gmail.com>; Marcel Ramos <mram...@gmail.com>; cbiop...@googlegroups.com <cbiop...@googlegroups.com>; de Leeuw, Renee <rdel...@uic.edu>
Subject: Re: [cbioportal] Installation cBioPortalData error