su: ignoring --preserve-environment, it's mutually exclusive with --login ========================================================================================= UCSCXenaShiny version 2.2.0 Project URL: https://github.com/openbiox/UCSCXenaShiny Usages: https://openbiox.github.io/UCSCXenaShiny/ If you use it in published research, please cite: Shensuo Li, Yuzhong Peng, Minjun Chen, Yankun Zhao, Yi Xiong, Jianfeng Li, Peng Luo, Haitao Wang, Fei Zhao, Qi Zhao, Yanru Cui, Sujun Chen, Jian-Guo Zhou, Shixiang Wang, Facilitating integrative and personalized oncology omics analysis with UCSCXenaShiny, Communications Biology, 1200 (2024), https://doi.org/10.1038/s42003-024-06891-2 ========================================================================================= --Enjoy it-- Run mode: server Checking dependencies... Loading required namespace: pacman Loading required namespace: gganatogram Loading modules and UIs... Starting... Listening on http://127.0.0.1:46393 Shiny app run successfully! Enjoy it! -- Xena shiny team Download datasets from server mode. Try querying data #1 -> Checking if the dataset has probeMap... -> Done. ProbeMap is found. Saving data to file /xena/cache/ec220112f497cf68f8da6d0980721724.rds More info about dataset please run following commands: library(UCSCXenaTools) XenaGenerate(subset = XenaDatasets == "TcgaTargetGtex_rsem_gene_tpm") %>% XenaBrowse() Joining with `by = join_by(sample)` Warning: Error in mutate: ℹ In argument: `p = purrr::map(...)`. Caused by error in `purrr::map()`: ℹ In index: 26. ℹ With name: tissue.MESO. Caused by error in `tidyr::pivot_longer()`: ! `cols` must select at least one column. 190: 189: signalCondition 188: signal_abort 187: abort 186: 185: signalCondition 184: signal_abort 183: rlang::abort 182: cli::cli_abort 181: 180: signalCondition 179: signal_abort 178: rlang::abort 177: cli::cli_abort 176: build_longer_spec 175: pivot_longer.data.frame 174: tidyr::pivot_longer 173: dplyr::select 172: dplyr::filter 171: %>% 170: .f 169: call_with_cleanup 168: withCallingHandlers 167: with_indexed_errors 166: map_ 165: purrr::map 164: eval 163: mask$eval_all_mutate 162: mutate_col 161: withCallingHandlers 160: mutate_cols 159: mutate.data.frame 158: mutate 157: select 156: %>% 155: df_select 154: tidyr::unnest 153: unnest 152: %>% 151: compare_means 150: dplyr::arrange 149: %>% 148: 147: ..stacktraceon.. 146: .func 145: withVisible 144: withCallingHandlers 143: contextFunc 142: env$runWith 141: withCallingHandlers 140: domain$wrapSync 139: promises::with_promise_domain 138: captureStackTraces 137: force 136: with_otel_span_context 135: force 134: domain$wrapSync 133: promises::with_promise_domain 132: withReactiveDomain 131: domain$wrapSync 130: promises::with_promise_domain 129: ctx$run 128: self$.updateValue 127: ..stacktraceoff.. 126: stat_res 125: paste0 124: dots_list 123: a 122: dots_list 121: tags$li 120: dots_list 119: tags$ul 118: dots_list 117: tagList 116: renderUI 115: func 114: ..stacktraceon.. 113: force 112: withVisible 111: withCallingHandlers 110: domain$wrapSync 109: promises::with_promise_domain 108: captureStackTraces 107: doTryCatch 106: tryCatchOne 105: tryCatchList 104: tryCatch 103: do 102: hybrid_chain 101: renderFunc 100: ..stacktraceoff.. 99: output$homepage_daily_gene-gene_tip 98: ..stacktraceon.. 97: orig 96: func 95: withCallingHandlers 94: domain$wrapSync 93: promises::with_promise_domain 92: captureStackTraces 91: withCallingHandlers 90: shinyCallingHandlers 89: force 88: with_otel_span_reactive_update 87: withCallingHandlers 86: doTryCatch 85: tryCatchOne 84: tryCatchList 83: base::tryCatch 82: tryCatch 81: withVisible 80: hybrid_then 79: maybe_with_otel_span_reactive_update 78: force 77: domain$wrapSync 76: with_promise_domain 75: private$withCurrentOutput 74: force 73: withVisible 72: withCallingHandlers 71: domain$wrapSync 70: promises::with_promise_domain 69: captureStackTraces 68: doTryCatch 67: tryCatchOne 66: tryCatchList 65: tryCatch 64: do 63: hybrid_chain 62: force 61: withVisible 60: withCallingHandlers 59: domain$wrapSync 58: promises::with_promise_domain 57: captureStackTraces 56: doTryCatch 55: tryCatchOne 54: tryCatchList 53: tryCatch 52: do 51: hybrid_chain 50: observe 49: 48: contextFunc 47: env$runWith 46: withCallingHandlers 45: domain$wrapSync 44: promises::with_promise_domain 43: captureStackTraces 42: force 41: with_otel_span_context 40: force 39: domain$wrapSync 38: promises::with_promise_domain 37: withReactiveDomain 36: domain$wrapSync 35: promises::with_promise_domain 34: ctx$run 33: run 32: withCallingHandlers 31: domain$wrapSync 30: promises::with_promise_domain 29: captureStackTraces 28: withCallingHandlers 27: shinyCallingHandlers 26: force 25: withVisible 24: withCallingHandlers 23: domain$wrapSync 22: promises::with_promise_domain 21: captureStackTraces 20: doTryCatch 19: tryCatchOne 18: tryCatchList 17: tryCatch 16: do 15: hybrid_chain 14: flushCallback 13: FUN 12: lapply 11: ctx$executeFlushCallbacks 10: .getReactiveEnvironment()$flush 9: flushReact 8: serviceApp 7: ..stacktracefloor.. 6: withCallingHandlers 5: domain$wrapSync 4: promises::with_promise_domain 3: captureStackTraces 2: ..stacktraceoff.. 1: runApp Warning: Error in dplyr::filter: ℹ In argument: `tissue == stat_res()$tissue[1]`. Caused by error in `mutate()`: ℹ In argument: `p = purrr::map(...)`. Caused by error in `purrr::map()`: ℹ In index: 26. ℹ With name: tissue.MESO. Caused by error in `tidyr::pivot_longer()`: ! `cols` must select at least one column. 138: 137: signalCondition 136: signal_abort 135: abort 134: 133: stop 132: stat_res 131: eval 130: mask$eval_all_filter 129: withCallingHandlers 128: filter_eval 127: filter_rows 126: filter_impl 125: filter.data.frame 124: dplyr::filter 123: dplyr::filter 122: ggboxplot 121: %>% 120: renderPlotly 119: func 118: promises::is.promising 117: getFromNamespace("prepareWidget", "plotly") 116: shinyRenderWidget 115: func 114: ..stacktraceon.. 113: force 112: withVisible 111: withCallingHandlers 110: domain$wrapSync 109: promises::with_promise_domain 108: captureStackTraces 107: doTryCatch 106: tryCatchOne 105: tryCatchList 104: tryCatch 103: do 102: hybrid_chain 101: renderFunc 100: ..stacktraceoff.. 99: output$homepage_daily_gene-box_plot 98: ..stacktraceon.. 97: orig 96: func 95: withCallingHandlers 94: domain$wrapSync 93: promises::with_promise_domain 92: captureStackTraces 91: withCallingHandlers 90: shinyCallingHandlers 89: force 88: with_otel_span_reactive_update 87: withCallingHandlers 86: doTryCatch 85: tryCatchOne 84: tryCatchList 83: base::tryCatch 82: tryCatch 81: withVisible 80: hybrid_then 79: maybe_with_otel_span_reactive_update 78: force 77: domain$wrapSync 76: with_promise_domain 75: private$withCurrentOutput 74: force 73: withVisible 72: withCallingHandlers 71: domain$wrapSync 70: promises::with_promise_domain 69: captureStackTraces 68: doTryCatch 67: tryCatchOne 66: tryCatchList 65: tryCatch 64: do 63: hybrid_chain 62: force 61: withVisible 60: withCallingHandlers 59: domain$wrapSync 58: promises::with_promise_domain 57: captureStackTraces 56: doTryCatch 55: tryCatchOne 54: tryCatchList 53: tryCatch 52: do 51: hybrid_chain 50: observe 49: 48: contextFunc 47: env$runWith 46: withCallingHandlers 45: domain$wrapSync 44: promises::with_promise_domain 43: captureStackTraces 42: force 41: with_otel_span_context 40: force 39: domain$wrapSync 38: promises::with_promise_domain 37: withReactiveDomain 36: domain$wrapSync 35: promises::with_promise_domain 34: ctx$run 33: run 32: withCallingHandlers 31: domain$wrapSync 30: promises::with_promise_domain 29: captureStackTraces 28: withCallingHandlers 27: shinyCallingHandlers 26: force 25: withVisible 24: withCallingHandlers 23: domain$wrapSync 22: promises::with_promise_domain 21: captureStackTraces 20: doTryCatch 19: tryCatchOne 18: tryCatchList 17: tryCatch 16: do 15: hybrid_chain 14: flushCallback 13: FUN 12: lapply 11: ctx$executeFlushCallbacks 10: .getReactiveEnvironment()$flush 9: flushReact 8: serviceApp 7: ..stacktracefloor.. 6: withCallingHandlers 5: domain$wrapSync 4: promises::with_promise_domain 3: captureStackTraces 2: ..stacktraceoff.. 1: runApp This will check url status, please be patient. This will check url status, please be patient. This will check url status, please be patient. Shiny app run successfully! Enjoy it! -- Xena shiny team Download datasets from server mode. Reading cache data /xena/cache/ec220112f497cf68f8da6d0980721724.rds More info about dataset please run following commands: library(UCSCXenaTools) XenaGenerate(subset = XenaDatasets == "TcgaTargetGtex_rsem_gene_tpm") %>% XenaBrowse() Joining with `by = join_by(sample)` Warning: Error in mutate: ℹ In argument: `p = purrr::map(...)`. Caused by error in `purrr::map()`: ℹ In index: 26. ℹ With name: tissue.MESO. Caused by error in `tidyr::pivot_longer()`: ! `cols` must select at least one column. 190: 189: signalCondition 188: signal_abort 187: abort 186: 185: signalCondition 184: signal_abort 183: rlang::abort 182: cli::cli_abort 181: 180: signalCondition 179: signal_abort 178: rlang::abort 177: cli::cli_abort 176: build_longer_spec 175: pivot_longer.data.frame 174: tidyr::pivot_longer 173: dplyr::select 172: dplyr::filter 171: %>% 170: .f 169: call_with_cleanup 168: withCallingHandlers 167: with_indexed_errors 166: map_ 165: purrr::map 164: eval 163: mask$eval_all_mutate 162: mutate_col 161: withCallingHandlers 160: mutate_cols 159: mutate.data.frame 158: mutate 157: select 156: %>% 155: df_select 154: tidyr::unnest 153: unnest 152: %>% 151: compare_means 150: dplyr::arrange 149: %>% 148: 147: ..stacktraceon.. 146: .func 145: withVisible 144: withCallingHandlers 143: contextFunc 142: env$runWith 141: withCallingHandlers 140: domain$wrapSync 139: promises::with_promise_domain 138: captureStackTraces 137: force 136: with_otel_span_context 135: force 134: domain$wrapSync 133: promises::with_promise_domain 132: withReactiveDomain 131: domain$wrapSync 130: promises::with_promise_domain 129: ctx$run 128: self$.updateValue 127: ..stacktraceoff.. 126: stat_res 125: paste0 124: dots_list 123: a 122: dots_list 121: tags$li 120: dots_list 119: tags$ul 118: dots_list 117: tagList 116: renderUI 115: func 114: ..stacktraceon.. 113: force 112: withVisible 111: withCallingHandlers 110: domain$wrapSync 109: promises::with_promise_domain 108: captureStackTraces 107: doTryCatch 106: tryCatchOne 105: tryCatchList 104: tryCatch 103: do 102: hybrid_chain 101: renderFunc 100: ..stacktraceoff.. 99: output$homepage_daily_gene-gene_tip 98: ..stacktraceon.. 97: orig 96: func 95: withCallingHandlers 94: domain$wrapSync 93: promises::with_promise_domain 92: captureStackTraces 91: withCallingHandlers 90: shinyCallingHandlers 89: force 88: with_otel_span_reactive_update 87: withCallingHandlers 86: doTryCatch 85: tryCatchOne 84: tryCatchList 83: base::tryCatch 82: tryCatch 81: withVisible 80: hybrid_then 79: maybe_with_otel_span_reactive_update 78: force 77: domain$wrapSync 76: with_promise_domain 75: private$withCurrentOutput 74: force 73: withVisible 72: withCallingHandlers 71: domain$wrapSync 70: promises::with_promise_domain 69: captureStackTraces 68: doTryCatch 67: tryCatchOne 66: tryCatchList 65: tryCatch 64: do 63: hybrid_chain 62: force 61: withVisible 60: withCallingHandlers 59: domain$wrapSync 58: promises::with_promise_domain 57: captureStackTraces 56: doTryCatch 55: tryCatchOne 54: tryCatchList 53: tryCatch 52: do 51: hybrid_chain 50: observe 49: 48: contextFunc 47: env$runWith 46: withCallingHandlers 45: domain$wrapSync 44: promises::with_promise_domain 43: captureStackTraces 42: force 41: with_otel_span_context 40: force 39: domain$wrapSync 38: promises::with_promise_domain 37: withReactiveDomain 36: domain$wrapSync 35: promises::with_promise_domain 34: ctx$run 33: run 32: withCallingHandlers 31: domain$wrapSync 30: promises::with_promise_domain 29: captureStackTraces 28: withCallingHandlers 27: shinyCallingHandlers 26: force 25: withVisible 24: withCallingHandlers 23: domain$wrapSync 22: promises::with_promise_domain 21: captureStackTraces 20: doTryCatch 19: tryCatchOne 18: tryCatchList 17: tryCatch 16: do 15: hybrid_chain 14: flushCallback 13: FUN 12: lapply 11: ctx$executeFlushCallbacks 10: .getReactiveEnvironment()$flush 9: flushReact 8: serviceApp 7: ..stacktracefloor.. 6: withCallingHandlers 5: domain$wrapSync 4: promises::with_promise_domain 3: captureStackTraces 2: ..stacktraceoff.. 1: runApp Warning: Error in dplyr::filter: ℹ In argument: `tissue == stat_res()$tissue[1]`. Caused by error in `mutate()`: ℹ In argument: `p = purrr::map(...)`. Caused by error in `purrr::map()`: ℹ In index: 26. ℹ With name: tissue.MESO. Caused by error in `tidyr::pivot_longer()`: ! `cols` must select at least one column. 138: 137: signalCondition 136: signal_abort 135: abort 134: 133: stop 132: stat_res 131: eval 130: mask$eval_all_filter 129: withCallingHandlers 128: filter_eval 127: filter_rows 126: filter_impl 125: filter.data.frame 124: dplyr::filter 123: dplyr::filter 122: ggboxplot 121: %>% 120: renderPlotly 119: func 118: promises::is.promising 117: getFromNamespace("prepareWidget", "plotly") 116: shinyRenderWidget 115: func 114: ..stacktraceon.. 113: force 112: withVisible 111: withCallingHandlers 110: domain$wrapSync 109: promises::with_promise_domain 108: captureStackTraces 107: doTryCatch 106: tryCatchOne 105: tryCatchList 104: tryCatch 103: do 102: hybrid_chain 101: renderFunc 100: ..stacktraceoff.. 99: output$homepage_daily_gene-box_plot 98: ..stacktraceon.. 97: orig 96: func 95: withCallingHandlers 94: domain$wrapSync 93: promises::with_promise_domain 92: captureStackTraces 91: withCallingHandlers 90: shinyCallingHandlers 89: force 88: with_otel_span_reactive_update 87: withCallingHandlers 86: doTryCatch 85: tryCatchOne 84: tryCatchList 83: base::tryCatch 82: tryCatch 81: withVisible 80: hybrid_then 79: maybe_with_otel_span_reactive_update 78: force 77: domain$wrapSync 76: with_promise_domain 75: private$withCurrentOutput 74: force 73: withVisible 72: withCallingHandlers 71: domain$wrapSync 70: promises::with_promise_domain 69: captureStackTraces 68: doTryCatch 67: tryCatchOne 66: tryCatchList 65: tryCatch 64: do 63: hybrid_chain 62: force 61: withVisible 60: withCallingHandlers 59: domain$wrapSync 58: promises::with_promise_domain 57: captureStackTraces 56: doTryCatch 55: tryCatchOne 54: tryCatchList 53: tryCatch 52: do 51: hybrid_chain 50: observe 49: 48: contextFunc 47: env$runWith 46: withCallingHandlers 45: domain$wrapSync 44: promises::with_promise_domain 43: captureStackTraces 42: force 41: with_otel_span_context 40: force 39: domain$wrapSync 38: promises::with_promise_domain 37: withReactiveDomain 36: domain$wrapSync 35: promises::with_promise_domain 34: ctx$run 33: run 32: withCallingHandlers 31: domain$wrapSync 30: promises::with_promise_domain 29: captureStackTraces 28: withCallingHandlers 27: shinyCallingHandlers 26: force 25: withVisible 24: withCallingHandlers 23: domain$wrapSync 22: promises::with_promise_domain 21: captureStackTraces 20: doTryCatch 19: tryCatchOne 18: tryCatchList 17: tryCatch 16: do 15: hybrid_chain 14: flushCallback 13: FUN 12: lapply 11: ctx$executeFlushCallbacks 10: .getReactiveEnvironment()$flush 9: flushReact 8: serviceApp 7: ..stacktracefloor.. 6: withCallingHandlers 5: domain$wrapSync 4: promises::with_promise_domain 3: captureStackTraces 2: ..stacktraceoff.. 1: runApp This will check url status, please be patient. Check ProbeMap urls of datasets. All downloaded files will under directory /xena/cache/datasets. Downloading TCGA.ESCA.sampleMap__HiSeqV2_PANCAN.gz trying URL 'https://tcga.xenahubs.net/download/TCGA.ESCA.sampleMap/HiSeqV2_PANCAN.gz' Content type 'binary/octet-stream' length 15164241 bytes (14.5 MB) = downloaded 339 KB ==> Trying #2 trying URL 'https://tcga.xenahubs.net/download/TCGA.ESCA.sampleMap/HiSeqV2_PANCAN.gz' Content type 'binary/octet-stream' length 15164241 bytes (14.5 MB) = downloaded 475 KB ==> Trying #3 trying URL 'https://tcga.xenahubs.net/download/TCGA.ESCA.sampleMap/HiSeqV2_PANCAN.gz' Content type 'binary/octet-stream' length 15164241 bytes (14.5 MB) = downloaded 492 KB Tried 3 times but failed, please check your internet connection! Downloading probeMap__hugo_gencode_good_hg19_V24lift37_probemap trying URL 'https://tcga.xenahubs.net/download/probeMap/hugo_gencode_good_hg19_V24lift37_probemap' Content type 'binary/octet-stream' length 5281731 bytes (5.0 MB) ===== downloaded 560 KB ==> Trying #2 trying URL 'https://tcga.xenahubs.net/download/probeMap/hugo_gencode_good_hg19_V24lift37_probemap' Content type 'binary/octet-stream' length 5281731 bytes (5.0 MB) == downloaded 220 KB ==> Trying #3 trying URL 'https://tcga.xenahubs.net/download/probeMap/hugo_gencode_good_hg19_V24lift37_probemap' Content type 'binary/octet-stream' length 5281731 bytes (5.0 MB) ===== downloaded 594 KB Tried 3 times but failed, please check your internet connection! Note file names inherit from names in datasets column and '/' all changed to '__'. Execution halted