404 not found error in dataman_2019.Rmd about labs HOT 4 OPEN

On Mon, Sep 9, 2019 at 9:45 PM gillsignals ***@***.***> wrote: Lines 875-877 of dataman_2019.Rmd generate a 404 not found error after authenticating with Google BigQuery and returning to R as directed by the browser: tcgaCon %>% tbl("Somatic_Mutation") %>% dplyr::filter(project_short_name=="TCGA-GBM") %>% dplyr::select(Variant_Classification, Hugo_Symbol) %>% group_by(Variant_Classification) %>% summarise(n=n()) Error: HTTP error [404] Not Found Is this the appropriate workflow? If so, what do learners need to know or do in order to not encounter this 404 error? > 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 stats4 parallel stats graphics grDevices utils datasets methods base other attached packages: [1] magrittr_1.5 dplyr_0.8.3 [3] bigrquery_1.2.0 RaggedExperiment_1.8.0 [5] curatedTCGAData_1.6.0 MultiAssayExperiment_1.10.4 [7] VariantTools_1.26.0 VariantAnnotation_1.30.1 [9] ph525x_0.0.48 png_0.1-7 [11] ldblock_1.14.2 erma_1.0.0 [13] Homo.sapiens_1.3.1 TxDb.Hsapiens.UCSC.hg19.knownGene_3.2.2 [15] OrganismDbi_1.26.0 GenomicFeatures_1.36.4 [17] GenomicAlignments_1.20.1 GenomicFiles_1.20.0 [19] rtracklayer_1.44.2 Rsamtools_2.0.0 [21] RNAseqData.HNRNPC.bam.chr14_0.22.0 IlluminaHumanMethylation450kanno.ilmn12.hg19_0.6.0 [23] IlluminaHumanMethylation450kmanifest_0.4.0 minfi_1.30.0 [25] bumphunter_1.26.0 locfit_1.5-9.1 [27] iterators_1.0.12 foreach_1.4.7 [29] Biostrings_2.52.0 XVector_0.24.0 [31] data.table_1.12.2 GO.db_3.8.2 [33] org.Hs.eg.db_3.8.2 airway_1.4.0 [35] SummarizedExperiment_1.14.1 DelayedArray_0.10.0 [37] BiocParallel_1.18.1 matrixStats_0.54.0 [39] GenomicRanges_1.36.0 GenomeInfoDb_1.20.0 [41] ArrayExpress_1.44.0 GEOquery_2.52.0 [43] annotate_1.62.0 XML_3.98-1.20 [45] AnnotationDbi_1.46.1 IRanges_2.18.1 [47] S4Vectors_0.22.0 Biobase_2.44.0 [49] BiocGenerics_0.30.0 GSE5859Subset_1.0 loaded via a namespace (and not attached): [1] tidyselect_0.2.5 RSQLite_2.1.2 munsell_0.5.0 codetools_0.2-16 [5] preprocessCore_1.46.0 withr_2.1.2 colorspace_1.4-1 knitr_1.24 [9] rstudioapi_0.10 labeling_0.3 GenomeInfoDbData_1.2.1 bit64_0.9-7 [13] rhdf5_2.28.0 vctrs_0.2.0 xfun_0.9 BiocFileCache_1.8.0 [17] affxparser_1.56.0 R6_2.4.0 illuminaio_0.26.0 AnnotationFilter_1.8.0 [21] bitops_1.0-6 reshape_0.8.8 assertthat_0.2.1 promises_1.0.1 [25] scales_1.0.0 gtable_0.3.0 ensembldb_2.8.0 rlang_0.4.0 [29] zeallot_0.1.0 genefilter_1.66.0 splines_3.6.1 lazyeval_0.2.2 [33] gargle_0.3.1 BiocManager_1.30.4 yaml_2.2.0 reshape2_1.4.3 [37] snpStats_1.34.0 backports_1.1.4 httpuv_1.5.1 RBGL_1.60.0 [41] tools_3.6.1 nor1mix_1.3-0 ggplot2_3.2.1 affyio_1.54.0 [45] ff_2.2-14 RColorBrewer_1.1-2 siggenes_1.58.0 Rcpp_1.0.1 [49] plyr_1.8.4 progress_1.2.2 zlibbioc_1.30.0 purrr_0.3.2 [53] RCurl_1.95-4.12 prettyunits_1.0.2 openssl_1.4.1 fs_1.3.1 [57] ProtGenerics_1.16.0 hms_0.5.1 mime_0.7 xtable_1.8-4 [61] mclust_5.4.5 gridExtra_2.3 compiler_3.6.1 biomaRt_2.40.4 [65] tibble_2.1.3 crayon_1.3.4 htmltools_0.3.6 later_0.8.0 [69] snow_0.4-3 tidyr_0.8.3 oligo_1.48.0 DBI_1.0.0 [73] ExperimentHub_1.10.0 dbplyr_1.4.2 MASS_7.3-51.4 rappdirs_0.3.1 [77] EnsDb.Hsapiens.v75_2.99.0 Matrix_1.2-17 readr_1.3.1 quadprog_1.5-7 [81] pkgconfig_2.0.2 registry_0.5-1 xml2_1.2.2 rngtools_1.4 [85] pkgmaker_0.27 multtest_2.40.0 beanplot_1.2 bibtex_0.4.2 [89] doRNG_1.7.1 scrime_1.3.5 stringr_1.4.0 digest_0.6.20 [93] graph_1.62.0 base64_2.0 DelayedMatrixStats_1.6.0 curl_4.0 [97] shiny_1.3.2 jsonlite_1.6 nlme_3.1-141 Rhdf5lib_1.6.0 [101] askpass_1.1 limma_3.40.6 BSgenome_1.52.0 pillar_1.4.2 [105] lattice_0.20-38 httr_1.4.1 survival_2.44-1.1 interactiveDisplayBase_1.22.0 [109] glue_1.3.1 UpSetR_1.4.0 bit_1.1-14 stringi_1.4.3 [113] HDF5Array_1.12.2 blob_1.2.0 oligoClasses_1.46.0 AnnotationHub_2.16.1 [117] memoise_1.1.0 Thanks! — You are receiving this because you are subscribed to this thread. Reply to this email directly, view it on GitHub <#82?email_source=notifications&email_token=ABDI5QRX2AYXVARKTO4HTR3QI333FA5CNFSM4IVB4AFKYY3PNVWWK3TUL52HS4DFUVEXG43VMWVGG33NNVSW45C7NFSM4HKKH4DQ>, or mute the thread <https://github.com/notifications/unsubscribe-auth/ABDI5QSB3ITANZV7WPXDIJLQI333FANCNFSM4IVB4AFA> .

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