TCGAbiolinks BioMart error
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Entering edit mode
Talip Zengin ▴ 10
@talip-zengin-14290
Last seen 11 months ago
Mugla, Turkiye

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             
> 
TCGAbiolinks BioMart • 535 views
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Entering edit mode
@james-w-macdonald-5106
Last seen 8 hours ago
United States

You are using a version of R that is more than a year out of date. Please update to R-4.0.1 and the current release version of Bioconductor and try again.

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Entering edit mode

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?

BiocManager::install("BioinformaticsFMRP/TCGAbiolinks", dependencies=TRUE)

... * installing source package ‘R.oo’ ... * package ‘R.oo’ successfully unpacked and MD5 sums checked * using staged installation * R * inst ** byte-compile and prepare package for lazy loading Error in RccViolationException("Class names must begin with a letter: ", :
"RccViolationException" function can not be found Error: unable to load R code in package ‘R.oo’ Stopped working ERROR: lazy loading failed for package ‘R.oo’ * removing ‘/truba/home/tzengin/R/lib64/R/library/R.oo’ Error: Failed to install 'TCGAbiolinks' from GitHub: installation of package ‘R.oo’ had non-zero exit status

install.packages("R.oo")

URL 'https://cran.rstudio.com/src/contrib/R.oo_1.23.0.tar.gz' trying Content type 'application/x-gzip' length 381285 bytes (372 KB) ================================================== downloaded 372 KB

installing source package ‘R.oo’ ... package ‘R.oo’ successfully unpacked and MD5 sums checked using staged installation R inst byte-compile and prepare package for lazy loading Error in RccViolationException("Class names must begin with a letter: ", :
"RccViolationException" command not found Error: unable to load R code in package ‘R.oo’ Stop working ERROR: lazy loading failed for package ‘R.oo’ * removing ‘/truba/home/tzengin/R/lib64/R/library/R.oo’

The downloaded source packages are in ‘/tmp/RtmpL6TpHe/downloaded_packages’ Updating HTML index of packages in '.Library' Making 'packages.html' ... done Warning message: In install.packages("R.oo") : installation of package ‘R.oo’ had non-zero exit status

sessionInfo()

R version 4.0.1 (2020-06-06) 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] LCCTYPE=trTR.UTF-8 LCNUMERIC=C
[3] LC
TIME=trTR.UTF-8 LCCOLLATE=trTR.UTF-8 [5] LCMONETARY=trTR.UTF-8 LCMESSAGES=trTR.UTF-8 [7] LCPAPER=trTR.UTF-8 LCNAME=C [9] LCADDRESS=C LCTELEPHONE=C [11] LCMEASUREMENT=trTR.UTF-8 LC_IDENTIFICATION=C

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

other attached packages: [1] remotes_2.2.0

loaded via a namespace (and not attached): [1] BiocManager1.30.10 compiler4.0.1 tools4.0.1 [4] curl4.3

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