Question

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

0

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mario.zanfardino ▴ 160

@mariozanfardino-15232

Last seen 4.4 years ago

Naples (Italy)

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

Run:

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

Result:

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

Any suggestions?

TCGAutils multiassayexperiment coad • 1.6k views

ADD COMMENT • link updated 6.5 years ago by Marcel Ramos 700 • written 6.5 years ago by mario.zanfardino ▴ 160

score 1 · Answer 1 · 2018-06-27

1

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Marcel Ramos 700

@marcel-ramos-7325

Last seen 4 weeks ago

United States

Hi Mario,

Can you please include your sessionInfo() ?

This works for me with Bioc-devel 3.8.

library(curatedTCGAData)
library(TCGAutils)

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

> sampleTables(coad)
$`COAD_CNASeq-20160128`

01 10 11 
68 55 13 

$`COAD_CNASNP-20160128`

 01  02  06  10  11 
449   1   1 373  90 

$`COAD_CNVSNP-20160128`

 01  02  06  10  11 
449   1   1 373  90

> BiocManager::version()
[1] ‘3.8’

-Marcel

ADD COMMENT • link 6.5 years ago Marcel Ramos 700

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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/libblas.so.3.7.1
LAPACK: /usr/lib/x86_64-linux-gnu/lapack/liblapack.so.3.7.1

locale:
 [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’

biocLite("BiocUpgrade")
Error: Bioconductor version 3.8 cannot be upgraded with R version 3.5.0

ADD REPLY • link 6.5 years ago mario.zanfardino ▴ 160

1

Entering edit mode

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:

BiocInstaller::biocLite("TCGAutils")

Regards, Marcel

ADD REPLY • link 6.5 years ago Marcel Ramos 700

1

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Ok, now works. Thank you Marcel!

ADD REPLY • link 6.5 years ago mario.zanfardino ▴ 160