Hello I am trying to analyse the RNA Seq data of the TCGA-PAAD Dataset. I am unable to go beyond the GDCPrepare step. I have written everything I have done so far. Hope it helps in troubleshooting. Any help and guidance is appreciated. Thank you.

# include your problematic code here with any corresponding output 
library(TCGAbiolinks)
library(EDASeq)


query <- GDCquery(project = "TCGA-PAAD", 
                  data.category = "Transcriptome Profiling", 
                  data.type = "Gene Expression Quantification", 
                  workflow.type = "STAR - Counts")


samplesDown <- getResults(query,cols = c("cases"))
dataTP <- TCGAquery_SampleTypes(barcode = samplesDown, typesample = "TP")
dataNT <- TCGAquery_SampleTypes(barcode = samplesDown, typesample = "NT")


queryDown <- GDCquery(project = "TCGA-PAAD",
                      data.category = "Transcriptome Profiling",
                      data.type = "Gene Expression Quantification",
                      workflow.type = "STAR - Counts",
                      barcode = c(dataTP, dataNT))


GDCdownload(query = queryDown,
            files.per.chunk = 5)
data_Prep1 <- GDCprepare(query = queryDown, 
                         save = TRUE, 
                         save.filename = "TCGA_PAAD.rda")


# please also include the results of running the following in an R session 
1. query <- GDCquery(project = "TCGA-PAAD", 
                  data.category = "Transcriptome Profiling", 
                  data.type = "Gene Expression Quantification", 
                  workflow.type = "HTSeq - Counts")
ERROR and SOLUTION - Please set a valid workflow.type argument from the list below:
  => STAR - Counts
Solution - Changed HTSeq - Counts to STAR - Counts. Code worked.

2. data_Prep1 <- GDCprepare(query = queryDown, 
                         save = TRUE, 
                         save.filename = "TCGA_PAAD.rda")
ERROR and NO SOLUTION - Run `rlang::last_error()` to see where the error occurred.
There were 50 or more warnings (use warnings() to see the first 50)

Ran rlang::last_error() - <error/rlang_error>
Error in `fn()`:
! Join columns must be present in data.
x Problem with `#gene`.
---
Backtrace:
 1. TCGAbiolinks::GDCprepare(query = queryDown, save = TRUE, save.filename = "TCGA_PAAD.rda")
 4. purrr::reduce(., left_join, by = "#gene")
 5. purrr:::reduce_impl(.x, .f, ..., .init = .init, .dir = .dir)
 7. dplyr:::left_join.data.frame(out, elt, ...)


sessionInfo( )
R version 4.0.3 (2020-10-10)
Platform: x86_64-w64-mingw32/x64 (64-bit)
Running under: Windows 10 x64 (build 19044)

Matrix products: default

locale:
[1] LC_COLLATE=English_United States.1252  LC_CTYPE=English_United States.1252    LC_MONETARY=English_United States.1252
[4] LC_NUMERIC=C                           LC_TIME=English_United States.1252    

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

other attached packages:
 [1] EDASeq_2.24.0               ShortRead_1.48.0            GenomicAlignments_1.26.0    SummarizedExperiment_1.20.0
 [5] MatrixGenerics_1.2.1        matrixStats_0.62.0          Rsamtools_2.6.0             GenomicRanges_1.42.0       
 [9] GenomeInfoDb_1.26.7         Biostrings_2.58.0           XVector_0.30.0              IRanges_2.24.1             
[13] S4Vectors_0.28.1            BiocParallel_1.24.1         Biobase_2.50.0              BiocGenerics_0.36.1        
[17] TCGAbiolinks_2.18.0        

loaded via a namespace (and not attached):
 [1] bitops_1.0-7                bit64_4.0.5                 RColorBrewer_1.1-3          progress_1.2.2             
 [5] httr_1.4.4                  tools_4.0.3                 utf8_1.2.2                  R6_2.5.1                   
 [9] DBI_1.1.3                   colorspace_2.0-3            tidyselect_1.1.2            prettyunits_1.1.1          
[13] bit_4.0.4                   curl_4.3.2                  compiler_4.0.3              cli_3.2.0                  
[17] rvest_1.0.3                 xml2_1.3.3                  DelayedArray_0.16.3         rtracklayer_1.49.5         
[21] scales_1.2.1                readr_2.1.2                 askpass_1.1                 rappdirs_0.3.3             
[25] stringr_1.4.1               digest_0.6.29               R.utils_2.12.0              jpeg_0.1-9                 
[29] pkgconfig_2.0.3             dbplyr_2.1.1                fastmap_1.1.0               rlang_1.0.2                
[33] rstudioapi_0.14             RSQLite_2.2.12              generics_0.1.3              hwriter_1.3.2.1            
[37] jsonlite_1.8.0              vroom_1.5.7                 dplyr_1.0.8                 R.oo_1.25.0                
[41] RCurl_1.98-1.6              magrittr_2.0.2              GenomeInfoDbData_1.2.4      interp_1.0-33              
[45] Matrix_1.4-1                Rcpp_1.0.8                  munsell_0.5.0               fansi_1.0.2                
[49] lifecycle_1.0.1             R.methodsS3_1.8.2           stringi_1.7.6               yaml_2.3.5                 
[53] zlibbioc_1.36.0             plyr_1.8.7                  BiocFileCache_1.14.0        grid_4.0.3                 
[57] blob_1.2.3                  crayon_1.5.1                deldir_1.0-6                lattice_0.20-45            
[61] GenomicFeatures_1.42.3      hms_1.1.2                   knitr_1.40                  pillar_1.8.1               
[65] TCGAbiolinksGUI.data_1.10.0 biomaRt_2.46.3              XML_3.99-0.9                glue_1.6.2                 
[69] downloader_0.4              latticeExtra_0.6-30         data.table_1.14.2           vctrs_0.3.8                
[73] png_0.1-7                   tzdb_0.2.0                  gtable_0.3.0                openssl_2.0.0              
[77] purrr_0.3.4                 tidyr_1.2.0                 assertthat_0.2.1            cachem_1.0.6               
[81] ggplot2_3.3.6               aroma.light_3.20.0          xfun_0.30                   tibble_3.1.6               
[85] tinytex_0.41                AnnotationDbi_1.52.0        memoise_2.0.1               ellipsis_0.3.2