Question: TCGAutils: Error in .checkBarcodes(barcodes) : barcode delimiters not consistent
gravatar for mario.zanfardino
17 months ago by
Naples (Italy)
mario.zanfardino150 wrote:

I'm trying TCGAutils with coad dataset, but i have an error on sampleTables


coad <- curatedTCGAData::curatedTCGAData(diseaseCode = "COAD", assays = "CN*", = FALSE)


Error in .checkBarcodes(barcodes) : barcode delimiters not consistent

Any suggestions?


ADD COMMENTlink modified 17 months ago by Marcel Ramos ♦♦ 410 • written 17 months ago by mario.zanfardino150
Answer: TCGAutils: Error in .checkBarcodes(barcodes) : barcode delimiters not consistent
gravatar for Marcel Ramos
17 months ago by
Marcel Ramos ♦♦ 410
United States
Marcel Ramos ♦♦ 410 wrote:

Hi Mario,

Can you please include your sessionInfo() ?

This works for me with Bioc-devel 3.8.


coad <- curatedTCGAData("COAD", "CN*", FALSE)
> sampleTables(coad)

01 10 11 
68 55 13 


 01  02  06  10  11 
449   1   1 373  90 


 01  02  06  10  11 
449   1   1 373  90
> BiocManager::version()
[1] ‘3.8’


ADD COMMENTlink written 17 months ago by Marcel Ramos ♦♦ 410
R version 3.5.0 (2018-04-23)
Platform: x86_64-pc-linux-gnu (64-bit)
Running under: Ubuntu 18.04 LTS

Matrix products: default
BLAS: /usr/lib/x86_64-linux-gnu/blas/
LAPACK: /usr/lib/x86_64-linux-gnu/lapack/

 [1] LC_CTYPE=en_US.UTF-8       LC_NUMERIC=C               LC_TIME=it_IT.UTF-8        LC_COLLATE=en_US.UTF-8     LC_MONETARY=it_IT.UTF-8    LC_MESSAGES=en_US.UTF-8   
 [7] LC_PAPER=it_IT.UTF-8       LC_NAME=C                  LC_ADDRESS=C               LC_TELEPHONE=C             LC_MEASUREMENT=it_IT.UTF-8 LC_IDENTIFICATION=C       

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

other attached packages:
 [1] RTCGAToolbox_2.10.0        RaggedExperiment_1.4.0     GenomicRanges_1.32.3       GenomeInfoDb_1.16.0        IRanges_2.14.10            S4Vectors_0.18.3          
 [7] BiocGenerics_0.26.0        curatedTCGAData_1.2.0      TCGAutils_1.0.1            bindrcpp_0.2.2             shinythemes_1.1.1          heatmaply_0.15.0          
[13] viridis_0.5.1              viridisLite_0.3.0          shinydashboard_0.7.0       cowplot_0.9.2              shinycssloaders_0.2.0      crosstalk_1.0.0           
[19] plotly_4.7.1               ggplot2_2.2.1              readr_1.1.1                dplyr_0.7.5                shinyjs_1.0                DT_0.4                    
[25] shiny_1.1.0                MultiAssayExperiment_1.6.0 BiocInstaller_1.30.0      

loaded via a namespace (and not attached):
  [1] colorspace_1.3-2              class_7.3-14                  modeltools_0.2-21             mclust_5.4.1                  XVector_0.20.0               
  [6] flexmix_2.3-14                bit64_0.9-7                   interactiveDisplayBase_1.18.0 AnnotationDbi_1.42.1          mvtnorm_1.0-8                
 [11] xml2_1.2.0                    splines_3.5.0                 codetools_0.2-15              robustbase_0.93-1             config_0.3                   
 [16] jsonlite_1.5                  cluster_2.0.7-1               kernlab_0.9-26                compiler_3.5.0                httr_1.3.1                   
 [21] assertthat_0.2.0              Matrix_1.2-14                 lazyeval_0.2.1                limma_3.36.2                  later_0.7.3                  
 [26] htmltools_0.3.6               tools_3.5.0                   gtable_0.2.0                  glue_1.2.0                    GenomeInfoDbData_1.1.0       
 [31] rappdirs_0.3.1                Rcpp_0.12.17                  Biobase_2.40.0                trimcluster_0.1-2             RJSONIO_1.3-0                
 [36] gdata_2.18.0                  ExperimentHub_1.6.0           iterators_1.0.9               fpc_2.1-11                    stringr_1.3.1                
 [41] rvest_0.3.2                   mime_0.5                      gtools_3.8.1                  XML_3.98-1.11                 dendextend_1.8.0             
 [46] AnnotationHub_2.12.0          DEoptimR_1.0-8                RCircos_1.2.0                 zlibbioc_1.26.0               MASS_7.3-50                  
 [51] scales_0.5.0                  TSP_1.1-6                     hms_0.4.2                     promises_1.0.1                SummarizedExperiment_1.10.1  
 [56] RColorBrewer_1.1-2            curl_3.2                      yaml_2.1.19                   memoise_1.1.0                 gridExtra_2.3                
 [61] stringi_1.2.3                 RSQLite_2.1.1                 GenomicDataCommons_1.4.1      gclus_1.3.1                   foreach_1.4.4                
 [66] seriation_1.2-3               caTools_1.17.1                BiocParallel_1.14.1           rlang_0.2.1                   pkgconfig_2.0.1              
 [71] prabclus_2.2-6                matrixStats_0.53.1            bitops_1.0-6                  lattice_0.20-35               purrr_0.2.5                  
 [76] bindr_0.1.1                   htmlwidgets_1.2               bit_1.1-14                    tidyselect_0.2.4              plyr_1.8.4                   
 [81] magrittr_1.5                  R6_2.2.2                      gplots_3.0.1                  DelayedArray_0.6.1            DBI_1.0.0                    
 [86] pillar_1.2.3                  whisker_0.3-2                 survival_2.42-3               RCurl_1.95-4.10               nnet_7.3-12                  
 [91] tibble_1.4.2                  KernSmooth_2.23-15            grid_3.5.0                    data.table_1.11.4             blob_1.1.1                   
 [96] digest_0.6.15                 diptest_0.75-7                webshot_0.5.0                 xtable_1.8-2                  tidyr_0.8.1                  
[101] httpuv_1.4.4.1                munsell_0.5.0                 registry_0.5    


> BiocManager::version()
[1] ‘3.7’
Error: Bioconductor version 3.8 cannot be upgraded with R version 3.5.0
ADD REPLYlink modified 17 months ago • written 17 months ago by mario.zanfardino150

Hi Mario, I've checked this with the Bioconductor release version 3.7 and it works as well.

There may be something wrong with your installation. Check that you're not mixing versions of packages.

Remove a couple of packages: remove.packages(c("BiocManager", "BiocVersion")).

Your biocLite("BiocUpgrade") should return something like:

> BiocInstaller::biocLite("BiocUpgrade")
Error: Bioconductor version 3.7 can be upgraded, but only to 'devel'; see ?useDevel.
  Use biocLite() without any arguments to update installed packages

Then, reinstall TCGAutils using BiocInstaller:


Regards, Marcel

ADD REPLYlink modified 17 months ago • written 17 months ago by Marcel Ramos ♦♦ 410

Ok, now works. Thank you Marcel!

ADD REPLYlink written 17 months ago by mario.zanfardino150
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