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Hi, I am using TCGAbiolinks and get BioMart error while running GDCprepare command. I reinstalled TCGAbiolinks and BioMart but got same error. My commands and session info are below. How can I solve this problem? Thanks in advance.
library(TCGAbiolinks)
library(SummarizedExperiment)
library(dplyr)
library(DT)
query_exp <- GDCquery(project = "TCGA-LUAD",
data.category = "Transcriptome Profiling",
data.type = "Gene Expression Quantification",
workflow.type = "HTSeq - Counts",
barcode = common_patients)
GDCdownload(query_exp, files.per.chunk = 100)
GeneExp <- GDCprepare(query_exp)
save(GeneExp, file ="_GeneExp.rda")
> |====================================================|100% Completed after 38 s
> Starting to add information to samples
> => Add clinical information to samples
> => Adding TCGA molecular information from marker papers
> => Information will have prefix 'paper_'
> luad subtype information from:doi:10.1038/nature13385
> Accessing www.ensembl.org to get gene information
> Error in get.GRCh.bioMart("hg38") : failed to get URL after 3 tries:
> error: Unexpected format to the list of available marts.
> Please check the following URL manually, and try ?listMarts for advice.
> http://uswest.ensembl.org:80/biomart/martservice?type=registry&requestid=biomaRt
> Ek olarak: Warning messages:
> 1: In mapCurlOptNames(names(.els), asNames = TRUE) :
> Unrecognized CURL options: followlocation, ssl.verifypeer, writefunction
> 2: In mapCurlOptNames(names(.els), asNames = TRUE) :
> Unrecognized CURL options: followlocation, ssl.verifypeer, writefunction
> 3: In mapCurlOptNames(names(.els), asNames = TRUE) :
> Unrecognized CURL options: followlocation, ssl.verifypeer, writefunction
BiocManager::install("BioinformaticsFMRP/TCGAbiolinks")
BiocManager::install("biomaRt")
sessionInfo()
> R version 3.5.2 (2018-12-20)
> Platform: x86_64-pc-linux-gnu (64-bit)
> Running under: CentOS Linux 7 (Core)
>
> Matrix products: default
> BLAS: /truba/home/tzengin/R/lib64/R/lib/libRblas.so
> LAPACK: /truba/home/tzengin/R/lib64/R/lib/libRlapack.so
>
> locale:
> [1] LC_CTYPE=tr_TR.UTF-8 LC_NUMERIC=C
> [3] LC_TIME=tr_TR.UTF-8 LC_COLLATE=tr_TR.UTF-8
> [5] LC_MONETARY=tr_TR.UTF-8 LC_MESSAGES=tr_TR.UTF-8
> [7] LC_PAPER=tr_TR.UTF-8 LC_NAME=C
> [9] LC_ADDRESS=C LC_TELEPHONE=C
> [11] LC_MEASUREMENT=tr_TR.UTF-8 LC_IDENTIFICATION=C
>
> attached base packages:
> [1] parallel stats4 stats graphics grDevices utils datasets
> [8] methods base
>
> other attached packages:
> [1] forcats_0.5.0 stringr_1.4.0
> [3] purrr_0.3.4 readr_1.3.1
> [5] tidyr_1.1.0 tibble_3.0.3
> [7] ggplot2_3.3.2 tidyverse_1.3.0
> [9] DT_0.14 dplyr_1.0.0
> [11] SummarizedExperiment_1.12.0 DelayedArray_0.8.0
> [13] BiocParallel_1.16.6 matrixStats_0.56.0
> [15] Biobase_2.42.0 GenomicRanges_1.34.0
> [17] GenomeInfoDb_1.18.2 IRanges_2.16.0
> [19] S4Vectors_0.20.1 BiocGenerics_0.28.0
> [21] TCGAbiolinks_2.17.3
>
> loaded via a namespace (and not attached):
> [1] httr_1.4.1 bit64_0.9-7.1 jsonlite_1.7.0
> [4] R.utils_2.8.0 modelr_0.1.8 assertthat_0.2.1
> [7] blob_1.2.1 cellranger_1.1.0 GenomeInfoDbData_1.2.0
> [10] progress_1.2.2 pillar_1.4.6 RSQLite_2.2.0
> [13] backports_1.1.8 lattice_0.20-41 glue_1.4.1
> [16] downloader_0.4 digest_0.6.25 XVector_0.22.0
> [19] rvest_0.3.5 colorspace_1.4-1 htmltools_0.5.0
> [22] Matrix_1.2-18 R.oo_1.22.0 plyr_1.8.6
> [25] XML_3.98-1.19 pkgconfig_2.0.3 broom_0.7.0
> [28] biomaRt_2.38.0 haven_2.3.1 zlibbioc_1.28.0
> [31] scales_1.1.1 generics_0.0.2 ellipsis_0.3.1
> [34] withr_2.2.0 cli_2.0.2 readxl_1.3.1
> [37] magrittr_1.5 crayon_1.3.4 memoise_1.1.0
> [40] R.methodsS3_1.8.0 fansi_0.4.1 fs_1.4.2
> [43] xml2_1.3.2 tools_3.5.2 data.table_1.12.8
> [46] prettyunits_1.1.1 hms_0.5.3 lifecycle_0.2.0
> [49] reprex_0.3.0 munsell_0.5.0 AnnotationDbi_1.44.0
> [52] compiler_3.5.2 rlang_0.4.7 grid_3.5.2
> [55] RCurl_1.98-1.2 rstudioapi_0.11 htmlwidgets_1.5.1
> [58] bitops_1.0-6 gtable_0.3.0 DBI_1.1.0
> [61] curl_4.3 R6_2.4.1 lubridate_1.7.9
> [64] knitr_1.29 bit_1.1-15.2 stringi_1.4.6
> [67] Rcpp_1.0.5 vctrs_0.3.2 dbplyr_1.4.4
> [70] tidyselect_1.1.0 xfun_0.15
>
Hi, Thanks for your advice. I tried both R-4.0.1 and R-4.0.2 but I got R.oo installation error below while installing TCGAbiolinks package. It is very surprising to get R package installation error in itself. How can I solve this problem?