Question: TCGAutils: Error in .checkBarcodes(barcodes) : barcode delimiters not consistent
0
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

Run:

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

Result:

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
1
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.

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 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/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 REPLYlink modified 17 months ago • written 17 months ago by mario.zanfardino150
1

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 REPLYlink modified 17 months ago • written 17 months ago by Marcel Ramos ♦♦ 410
1

Ok, now works. Thank you Marcel!

ADD REPLYlink written 17 months ago by mario.zanfardino150
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