getFirehoseData fails in tcga.Rmd: cannot open the connection

[gillsignals]

The TCGA firehose data download on tcga.Rmd line 49 throws an error stating the connection cannot be opened:

> library(ph525x)
> firehose()
> library(RTCGAToolbox)
> readData = getFirehoseData (dataset="READ", runDate="20150402",forceDownload = TRUE,
+     Clinic=TRUE, Mutation=TRUE, Methylation=TRUE, RNASeq2GeneNorm=TRUE)
gdac.broadinstitute.org_READ.Clinical_Pick_Tier1.Level_4.2015040200.0.0.tar.gz
trying URL 'http://gdac.broadinstitute.org/runs/stddata__2015_04_02/data/READ/20150402/gdac.broadinstitute.org_READ.Clinical_Pick_Tier1.Level_4.2015040200.0.0.tar.gz'
Content type 'application/x-gzip' length 4754 bytes
downloaded 4754 bytes

gdac.broadinstitute.org_READ.Clinical_Pick_Tier1.Level_4.2015040200.0.0
gdac.broadinstitute.org_READ.Merge_rnaseqv2__illuminaga_rnaseqv2__unc_edu__Level_3__RSEM_genes_normalized__data.Level_3.2015040200.0.0.tar.gzgdac.broadinstitute.org_READ.Merge_rnaseqv2__illuminahiseq_rnaseqv2__unc_edu__Level_3__RSEM_genes_normalized__data.Level_3.2015040200.0.0.tar.gz
trying URL 'http://gdac.broadinstitute.org/runs/stddata__2015_04_02/data/READ/20150402/gdac.broadinstitute.org_READ.Merge_rnaseqv2__illuminaga_rnaseqv2__unc_edu__Level_3__RSEM_genes_normalized__data.Level_3.2015040200.0.0.tar.gz'
Content type 'application/x-gzip' length 5917492 bytes (5.6 MB)
downloaded 5.6 MB

gdac.broadinstitute.org_READ.Merge_rnaseqv2__illuminaga_rnaseqv2__unc_edu__Level_3__RSEM_genes_normalized__data.Level_3.2015040200.0.0
cannot open file './20150402-READ-RNAseq2GeneNorm.txt': No such file or directoryError in file(file, "rt") : cannot open the connection

Much of the following code in the section and the related course videos depend on the output of this command.

In addition, the following code block on line 53 appears to read a local path on your machine.

Here is the sessionInfo:

> sessionInfo()
R version 3.6.1 (2019-07-05)
Platform: x86_64-w64-mingw32/x64 (64-bit)
Running under: Windows 10 x64 (build 17763)

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] grid      tools     parallel  stats4    stats     graphics  grDevices utils     datasets  methods   base     

other attached packages:
 [1] RTCGAToolbox_2.14.0                     ph525x_0.0.48                           png_0.1-7                              
 [4] yeastCC_1.24.0                          harbChIP_1.22.0                         Biostrings_2.52.0                      
 [7] XVector_0.24.0                          ERBS_1.0                                gwascat_2.16.0                         
[10] Homo.sapiens_1.3.1                      TxDb.Hsapiens.UCSC.hg19.knownGene_3.2.2 org.Hs.eg.db_3.8.2                     
[13] GO.db_3.8.2                             OrganismDbi_1.26.0                      GenomicFeatures_1.36.4                 
[16] GenomicRanges_1.36.0                    GenomeInfoDb_1.20.0                     ggbio_1.32.0                           
[19] ggplot2_3.2.1                           AnnotationDbi_1.46.1                    IRanges_2.18.1                         
[22] S4Vectors_0.22.0                        Biobase_2.44.0                          BiocGenerics_0.30.0                    

loaded via a namespace (and not attached):
 [1] ProtGenerics_1.16.0         bitops_1.0-6                matrixStats_0.54.0          bit64_0.9-7                
 [5] RColorBrewer_1.1-2          progress_1.2.2              httr_1.4.1                  backports_1.1.4            
 [9] R6_2.4.0                    rpart_4.1-15                Hmisc_4.2-0                 DBI_1.0.0                  
[13] lazyeval_0.2.2              colorspace_1.4-1            nnet_7.3-12                 withr_2.1.2                
[17] tidyselect_0.2.5            gridExtra_2.3               prettyunits_1.0.2           GGally_1.4.0               
[21] bit_1.1-14                  curl_4.0                    compiler_3.6.1              graph_1.62.0               
[25] htmlTable_1.13.1            DelayedArray_0.10.0         rtracklayer_1.44.2          scales_1.0.0               
[29] checkmate_1.9.4             RBGL_1.60.0                 RCircos_1.2.1               stringr_1.4.0              
[33] digest_0.6.20               Rsamtools_2.0.0             foreign_0.8-71              base64enc_0.1-3            
[37] dichromat_2.0-0             pkgconfig_2.0.2             htmltools_0.3.6             limma_3.40.6               
[41] ensembldb_2.8.0             BSgenome_1.52.0             htmlwidgets_1.3             rlang_0.4.0                
[45] rstudioapi_0.10             RSQLite_2.1.2               BiocParallel_1.18.1         acepack_1.4.1              
[49] dplyr_0.8.3                 VariantAnnotation_1.30.1    RCurl_1.95-4.12             magrittr_1.5               
[53] GenomeInfoDbData_1.2.1      Formula_1.2-3               Matrix_1.2-17               Rcpp_1.0.1                 
[57] munsell_0.5.0               stringi_1.4.3               RaggedExperiment_1.8.0      RJSONIO_1.3-1.2            
[61] SummarizedExperiment_1.14.1 zlibbioc_1.30.0             plyr_1.8.4                  blob_1.2.0                 
[65] crayon_1.3.4                lattice_0.20-38             splines_3.6.1               hms_0.5.1                  
[69] zeallot_0.1.0               knitr_1.24                  pillar_1.4.2                reshape2_1.4.3             
[73] biomaRt_2.40.4              XML_3.98-1.20               glue_1.3.1                  biovizBase_1.32.0          
[77] latticeExtra_0.6-28         BiocManager_1.30.4          data.table_1.12.2           vctrs_0.2.0                
[81] gtable_0.3.0                purrr_0.3.2                 reshape_0.8.8               assertthat_0.2.1           
[85] xfun_0.9                    AnnotationFilter_1.8.0      survival_2.44-1.1           tibble_2.1.3               
[89] GenomicAlignments_1.20.1    memoise_1.1.0               cluster_2.1.0 

Thanks!

[vjcitn]

we should try to rewrite using curatedTCGAData package who is handling video revisions?

…

On Mon, Aug 26, 2019 at 7:53 AM gillsignals ***@***.***> wrote: The TCGA firehose data download on tcga.Rmd line 49 <https://github.com/genomicsclass/labs/blob/9ac47c7099a8a2452813c4bb675c21010f5becec/biocadv_6x/tcga.Rmd#L49> throws an error stating the connection cannot be opened: > library(ph525x) > firehose() > library(RTCGAToolbox) > readData = getFirehoseData (dataset="READ", runDate="20150402",forceDownload = TRUE, + Clinic=TRUE, Mutation=TRUE, Methylation=TRUE, RNASeq2GeneNorm=TRUE) gdac.broadinstitute.org_READ.Clinical_Pick_Tier1.Level_4.2015040200.0.0.tar.gz trying URL 'http://gdac.broadinstitute.org/runs/stddata__2015_04_02/data/READ/20150402/gdac.broadinstitute.org_READ.Clinical_Pick_Tier1.Level_4.2015040200.0.0.tar.gz' Content type 'application/x-gzip' length 4754 bytes downloaded 4754 bytes gdac.broadinstitute.org_READ.Clinical_Pick_Tier1.Level_4.2015040200.0.0 gdac.broadinstitute.org_READ.Merge_rnaseqv2__illuminaga_rnaseqv2__unc_edu__Level_3__RSEM_genes_normalized__data.Level_3.2015040200.0.0.tar.gzgdac.broadinstitute.org_READ.Merge_rnaseqv2__illuminahiseq_rnaseqv2__unc_edu__Level_3__RSEM_genes_normalized__data.Level_3.2015040200.0.0.tar.gz trying URL 'http://gdac.broadinstitute.org/runs/stddata__2015_04_02/data/READ/20150402/gdac.broadinstitute.org_READ.Merge_rnaseqv2__illuminaga_rnaseqv2__unc_edu__Level_3__RSEM_genes_normalized__data.Level_3.2015040200.0.0.tar.gz' Content type 'application/x-gzip' length 5917492 bytes (5.6 MB) downloaded 5.6 MB gdac.broadinstitute.org_READ.Merge_rnaseqv2__illuminaga_rnaseqv2__unc_edu__Level_3__RSEM_genes_normalized__data.Level_3.2015040200.0.0 cannot open file './20150402-READ-RNAseq2GeneNorm.txt': No such file or directoryError in file(file, "rt") : cannot open the connection Much of the following code in the section and the related course videos depend on the output of this command. In addition, the following code block on line 53 appears to read a local path on your machine. Here is the sessionInfo: > sessionInfo() R version 3.6.1 (2019-07-05) Platform: x86_64-w64-mingw32/x64 (64-bit) Running under: Windows 10 x64 (build 17763) 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] grid tools parallel stats4 stats graphics grDevices utils datasets methods base other attached packages: [1] RTCGAToolbox_2.14.0 ph525x_0.0.48 png_0.1-7 [4] yeastCC_1.24.0 harbChIP_1.22.0 Biostrings_2.52.0 [7] XVector_0.24.0 ERBS_1.0 gwascat_2.16.0 [10] Homo.sapiens_1.3.1 TxDb.Hsapiens.UCSC.hg19.knownGene_3.2.2 org.Hs.eg.db_3.8.2 [13] GO.db_3.8.2 OrganismDbi_1.26.0 GenomicFeatures_1.36.4 [16] GenomicRanges_1.36.0 GenomeInfoDb_1.20.0 ggbio_1.32.0 [19] ggplot2_3.2.1 AnnotationDbi_1.46.1 IRanges_2.18.1 [22] S4Vectors_0.22.0 Biobase_2.44.0 BiocGenerics_0.30.0 loaded via a namespace (and not attached): [1] ProtGenerics_1.16.0 bitops_1.0-6 matrixStats_0.54.0 bit64_0.9-7 [5] RColorBrewer_1.1-2 progress_1.2.2 httr_1.4.1 backports_1.1.4 [9] R6_2.4.0 rpart_4.1-15 Hmisc_4.2-0 DBI_1.0.0 [13] lazyeval_0.2.2 colorspace_1.4-1 nnet_7.3-12 withr_2.1.2 [17] tidyselect_0.2.5 gridExtra_2.3 prettyunits_1.0.2 GGally_1.4.0 [21] bit_1.1-14 curl_4.0 compiler_3.6.1 graph_1.62.0 [25] htmlTable_1.13.1 DelayedArray_0.10.0 rtracklayer_1.44.2 scales_1.0.0 [29] checkmate_1.9.4 RBGL_1.60.0 RCircos_1.2.1 stringr_1.4.0 [33] digest_0.6.20 Rsamtools_2.0.0 foreign_0.8-71 base64enc_0.1-3 [37] dichromat_2.0-0 pkgconfig_2.0.2 htmltools_0.3.6 limma_3.40.6 [41] ensembldb_2.8.0 BSgenome_1.52.0 htmlwidgets_1.3 rlang_0.4.0 [45] rstudioapi_0.10 RSQLite_2.1.2 BiocParallel_1.18.1 acepack_1.4.1 [49] dplyr_0.8.3 VariantAnnotation_1.30.1 RCurl_1.95-4.12 magrittr_1.5 [53] GenomeInfoDbData_1.2.1 Formula_1.2-3 Matrix_1.2-17 Rcpp_1.0.1 [57] munsell_0.5.0 stringi_1.4.3 RaggedExperiment_1.8.0 RJSONIO_1.3-1.2 [61] SummarizedExperiment_1.14.1 zlibbioc_1.30.0 plyr_1.8.4 blob_1.2.0 [65] crayon_1.3.4 lattice_0.20-38 splines_3.6.1 hms_0.5.1 [69] zeallot_0.1.0 knitr_1.24 pillar_1.4.2 reshape2_1.4.3 [73] biomaRt_2.40.4 XML_3.98-1.20 glue_1.3.1 biovizBase_1.32.0 [77] latticeExtra_0.6-28 BiocManager_1.30.4 data.table_1.12.2 vctrs_0.2.0 [81] gtable_0.3.0 purrr_0.3.2 reshape_0.8.8 assertthat_0.2.1 [85] xfun_0.9 AnnotationFilter_1.8.0 survival_2.44-1.1 tibble_2.1.3 [89] GenomicAlignments_1.20.1 memoise_1.1.0 cluster_2.1.0 Thanks! — You are receiving this because you are subscribed to this thread. Reply to this email directly, view it on GitHub <#79?email_source=notifications&email_token=ABDI5QS7ITSMYVNEFO27K5LQGO735A5CNFSM4IPO3A52YY3PNVWWK3TUL52HS4DFUVEXG43VMWVGG33NNVSW45C7NFSM4HHLQNCA>, or mute the thread <https://github.com/notifications/unsubscribe-auth/ABDI5QR2L2EQJFOPLDZJB5DQGO735ANCNFSM4IPO3A5Q> .

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