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BioinformaticsFMRP / TCGAbiolinksGUI

TCGAbiolinksGUI code development for R/Bioconductor submission http://tcgabiolinks.fmrp.usp.br:3838/
http://bioinformaticsfmrp.github.io/TCGAbiolinksGUI
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TCGAbiolinksGUI() crashes on web browser #43

Open ghost opened 6 years ago

ghost commented 6 years ago

I used following commands on R Version 1.1.442 . library(TCGAbiolinksGUI) TCGAbiolinksGUI() It opens a web browser with address as below http://127.0.0.1:5209/ and then crashes. How to find solution ?

Jorges1000 commented 6 years ago

Me too.

Using Safari. Session Info: `R version 3.4.3 (2017-11-30) Platform: x86_64-apple-darwin15.6.0 (64-bit) Running under: macOS High Sierra 10.13.3

Matrix products: default BLAS: /System/Library/Frameworks/Accelerate.framework/Versions/A/Frameworks/vecLib.framework/Versions/A/libBLAS.dylib LAPACK: /Library/Frameworks/R.framework/Versions/3.4/Resources/lib/libRlapack.dylib

locale: [1] en_US.UTF-8/en_US.UTF-8/en_US.UTF-8/C/en_US.UTF-8/en_US.UTF-8

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

other attached packages: [1] BiocInstaller_1.28.0 dplyr_0.7.5 readr_1.1.1 htmlwidgets_1.2 ggrepel_0.8.0
[6] stringr_1.3.1 MultiAssayExperiment_1.4.9 clusterProfiler_3.6.0 DOSE_3.4.0 reshape2_1.4.3
[11] pathview_1.18.2 org.Hs.eg.db_3.5.0 AnnotationDbi_1.40.0 plotly_4.7.1 ggplot2_2.2.1
[16] SummarizedExperiment_1.8.1 DelayedArray_0.4.1 matrixStats_0.53.1 GenomicRanges_1.30.3 GenomeInfoDb_1.14.0
[21] IRanges_2.12.0 S4Vectors_0.16.0 shinyjs_1.0 shinyBS_0.61 TCGAbiolinks_2.6.12
[26] shinyFiles_0.7.0 shiny_1.1.0 TCGAbiolinksGUI_1.4.7 bigmemory_4.5.33 Biobase_2.38.0
[31] BiocGenerics_0.24.0 shinydashboard_0.7.0 splitstackshape_1.4.4 tibble_1.4.2 datapasta_3.0.0
[36] rlist_0.4.6.1 pipeR_0.6.1.3 data.table_1.11.4

loaded via a namespace (and not attached): [1] rtracklayer_1.38.3 ggthemes_3.5.0 R.methodsS3_1.7.1 pkgmaker_0.27
[5] tidyr_0.8.1 acepack_1.4.1 bit64_0.9-7 knitr_1.20
[9] aroma.light_3.8.0 R.utils_2.6.0 rpart_4.1-13 hwriter_1.3.2
[13] KEGGREST_1.18.1 RCurl_1.95-4.10 AnnotationFilter_1.2.0 doParallel_1.0.11
[17] GenomicFeatures_1.30.3 cowplot_0.9.2 RSQLite_2.1.1 bit_1.1-14
[21] xml2_1.2.0 httpuv_1.4.4.1 assertthat_0.2.0 hms_0.4.2
[25] promises_1.0.1 progress_1.2.0 Rgraphviz_2.22.0 km.ci_0.5-2
[29] igraph_1.2.1 DBI_1.0.0 geneplotter_1.56.0 reshape_0.8.7
[33] EDASeq_2.12.0 matlab_1.0.2 purrr_0.2.5 crosstalk_1.0.0
[37] selectr_0.4-1 ggpubr_0.1.6 backports_1.1.2 annotate_1.56.2
[41] gridBase_0.4-7 biomaRt_2.34.2 ensembldb_2.2.2 maftools_1.4.28
[45] withr_2.1.2 Gviz_1.22.3 BSgenome_1.46.0 checkmate_1.8.5
[49] GenomicAlignments_1.14.2 prettyunits_1.0.2 mclust_5.4 mnormt_1.5-5
[53] cluster_2.0.7 lazyeval_0.2.1 crayon_1.3.4 genefilter_1.60.0
[57] edgeR_3.20.9 pkgconfig_2.0.1 slam_0.1-43 nlme_3.1-137
[61] ProtGenerics_1.10.0 wordcloud_2.5 changepoint_2.2.2 nnet_7.3-12
[65] bindr_0.1.1 rlang_0.2.1 miniUI_0.1.1.1 colourpicker_1.0
[69] downloader_0.4 registry_0.5 bigmemory.sri_0.1.3 AnnotationHub_2.10.1
[73] dichromat_2.0-0 graph_1.56.0 rngtools_1.3.1 Matrix_1.2-13
[77] KMsurv_0.1-5 zoo_1.8-2 base64enc_0.1-3 GlobalOptions_0.1.0
[81] png_0.1-7 viridisLite_0.3.0 rjson_0.2.20 bitops_1.0-6
[85] R.oo_1.22.0 ConsensusClusterPlus_1.42.0 Biostrings_2.46.0 blob_1.1.1
[89] shape_1.4.4 qvalue_2.10.0 ShortRead_1.36.1 scales_0.5.0
[93] memoise_1.1.0 magrittr_1.5 plyr_1.8.4 bibtex_0.4.2
[97] zlibbioc_1.24.0 compiler_3.4.3 RColorBrewer_1.1-2 KEGGgraph_1.38.0
[101] Rsamtools_1.30.0 XVector_0.18.0 htmlTable_1.12 Formula_1.2-3
[105] mgcv_1.8-23 tidyselect_0.2.4 stringi_1.2.3 yaml_2.1.19
[109] GOSemSim_2.4.1 locfit_1.5-9.1 latticeExtra_0.6-28 survMisc_0.5.4
[113] VariantAnnotation_1.24.5 fastmatch_1.1-0 tools_3.4.3 circlize_0.4.4
[117] rstudioapi_0.7 foreach_1.4.4 foreign_0.8-69 gridExtra_2.3
[121] digest_0.6.15 rvcheck_0.1.0 cmprsk_2.2-7 bindrcpp_0.2.2
[125] Rcpp_0.12.17 broom_0.4.4 later_0.7.3 httr_1.3.1
[129] survminer_0.4.2 biovizBase_1.26.0 ComplexHeatmap_1.17.1 psych_1.8.4
[133] colorspace_1.3-2 rvest_0.3.2 XML_3.98-1.11 ELMER.data_2.2.2
[137] splines_3.4.3 xtable_1.8-2 jsonlite_1.5 ELMER_2.2.7
[141] R6_2.2.2 Hmisc_4.1-1 pillar_1.2.3 htmltools_0.3.6
[145] mime_0.5 NMF_0.21.0 DT_0.4 glue_1.2.0
[149] BiocParallel_1.12.0 RMySQL_0.10.15 DESeq_1.30.0 interactiveDisplayBase_1.16.0 [153] codetools_0.2-15 fgsea_1.4.1 lattice_0.20-35 sva_3.26.0
[157] curl_3.2 GO.db_3.5.0 survival_2.42-3 limma_3.34.9
[161] munsell_0.5.0 DO.db_2.9 GetoptLong_0.1.7 GenomeInfoDbData_1.0.0
[165] iterators_1.0.9 gtable_0.2.0 `

Sarabio81 commented 6 years ago

I have the same problem.

library("TCGAbiolinksGUI") TCGAbiolinksGUI() Warning: Error in if: argument is of length zero 48: survivalplotdata [C:/Users/Sara Ansari/Documents/R/win-library/3.5/TCGAbiolinksGUI/app/server/survival.R#30] 47: [C:/Users/Sara Ansari/Documents/R/win-library/3.5/TCGAbiolinksGUI/app/server/survival.R#72] 4: shiny::runApp 1: TCGAbiolinksGUI Warning: Error in if: argument is of length zero 48: survivalplotdata [C:/Users/Sara Ansari/Documents/R/win-library/3.5/TCGAbiolinksGUI/app/server/survival.R#30] 47: [C:/Users/Sara Ansari/Documents/R/win-library/3.5/TCGAbiolinksGUI/app/server/survival.R#84] 4: shiny::runApp 1: TCGAbiolinksGUI Warning: Error in if: argument is of length zero 48: survivalplotdata [C:/Users/Sara Ansari/Documents/R/win-library/3.5/TCGAbiolinksGUI/app/server/survival.R#30] 47: [C:/Users/Sara Ansari/Documents/R/win-library/3.5/TCGAbiolinksGUI/app/server/survival.R#99] 4: shiny::runApp 1: TCGAbiolinksGUI Warning: Error in if: argument is of length zero 47: [C:/Users/Sara Ansari/Documents/R/win-library/3.5/TCGAbiolinksGUI/app/server/volcano.R#99] 4: shiny::runApp 1: TCGAbiolinksGUI Warning: Error in if: argument is of length zero 64: [C:/Users/Sara Ansari/Documents/R/win-library/3.5/TCGAbiolinksGUI/app/server/volcano.R#62] 48: volcanodata 47: [C:/Users/Sara Ansari/Documents/R/win-library/3.5/TCGAbiolinksGUI/app/server/volcano.R#106] 4: shiny::runApp 1: TCGAbiolinksGUI Warning: Error in if: argument is of length zero 68: eval [C:/Users/Sara Ansari/Documents/R/win-library/3.5/TCGAbiolinksGUI/app/server/heatmap.R#164] 67: eval 66: withProgress 65: [C:/Users/Sara Ansari/Documents/R/win-library/3.5/TCGAbiolinksGUI/app/server/heatmap.R#161] 49: heatmapdata 47: [C:/Users/Sara Ansari/Documents/R/win-library/3.5/TCGAbiolinksGUI/app/server/heatmap.R#98] 4: shiny::runApp 1: TCGAbiolinksGUI Warning: Error in if: argument is of length zero 47: [C:/Users/Sara Ansari/Documents/R/win-library/3.5/TCGAbiolinksGUI/app/server/heatmap.R#111] 4: shiny::runApp 1: TCGAbiolinksGUI Warning: Error in if: argument is of length zero 50: Warning: Error in if: argument is of length zero 50: Warning: Error in if: argument is of length zero 96: eval [C:/Users/Sara Ansari/Documents/R/win-library/3.5/TCGAbiolinksGUI/app/server/dmr.R#153] 95: eval 94: withProgress 93: [C:/Users/Sara Ansari/Documents/R/win-library/3.5/TCGAbiolinksGUI/app/server/dmr.R#150] 77: dmrdata 75: observeEventHandler [C:/Users/Sara Ansari/Documents/R/win-library/3.5/TCGAbiolinksGUI/app/server/dmr.R#29] 4: shiny::runApp 1: TCGAbiolinksGUI Warning: Error in if: argument is of length zero 51: Warning: Error in if: argument is of length zero 68: eval [C:/Users/Sara Ansari/Documents/R/win-library/3.5/TCGAbiolinksGUI/app/server/meanMet.R#153] 67: eval 66: withProgress 65: [C:/Users/Sara Ansari/Documents/R/win-library/3.5/TCGAbiolinksGUI/app/server/meanMet.R#150] 49: meandata 47: [C:/Users/Sara Ansari/Documents/R/win-library/3.5/TCGAbiolinksGUI/app/server/meanMet.R#26] 4: shiny::runApp 1: TCGAbiolinksGUI Warning: Error in if: argument is of length zero 51: Warning: Error in gzfile: invalid 'description' argument 80: gzfile 79: load 77: deadata [C:/Users/Sara Ansari/Documents/R/win-library/3.5/TCGAbiolinksGUI/app/server/dea.R#165] 75: observeEventHandler [C:/Users/Sara Ansari/Documents/R/win-library/3.5/TCGAbiolinksGUI/app/server/dea.R#179] 4: shiny::runApp 1: TCGAbiolinksGUI Warning: Error in gzfile: invalid 'description' argument 80: gzfile 79: load 77: deadata [C:/Users/Sara Ansari/Documents/R/win-library/3.5/TCGAbiolinksGUI/app/server/dea.R#165] 75: observeEventHandler [C:/Users/Sara Ansari/Documents/R/win-library/3.5/TCGAbiolinksGUI/app/server/dea.R#186] 4: shiny::runApp 1: TCGAbiolinksGUI Warning: Error in gzfile: invalid 'description' argument 52: gzfile 51: load 49: deadata [C:/Users/Sara Ansari/Documents/R/win-library/3.5/TCGAbiolinksGUI/app/server/dea.R#165] 47: [C:/Users/Sara Ansari/Documents/R/win-library/3.5/TCGAbiolinksGUI/app/server/dea.R#194] 4: shiny::runApp 1: TCGAbiolinksGUI Warning: Error in if: argument is of length zero 66: [C:/Users/Sara Ansari/Documents/R/win-library/3.5/TCGAbiolinksGUI/app/server/oncoprint.R#112] 50: annotation.maf 47: [C:/Users/Sara Ansari/Documents/R/win-library/3.5/TCGAbiolinksGUI/app/server/oncoprint.R#90] 4: shiny::runApp 1: TCGAbiolinksGUI Warning: Error in gzfile: invalid 'description' argument 70: gzfile 69: load 64: [C:/Users/Sara Ansari/Documents/R/win-library/3.5/TCGAbiolinksGUI/app/server/elmer.R#347] 48: maedata 47: [C:/Users/Sara Ansari/Documents/R/win-library/3.5/TCGAbiolinksGUI/app/server/elmer.R#192] 4: shiny::runApp 1: TCGAbiolinksGUI Warning: Error in gzfile: invalid 'description' argument 78: Warning: Error in gzfile: invalid 'description' argument 78: Warning: Error in gzfile: invalid 'description' argument 70: gzfile 69: load 64: [C:/Users/Sara Ansari/Documents/R/win-library/3.5/TCGAbiolinksGUI/app/server/elmer.R#334] 48: elmer.results.data 47: [C:/Users/Sara Ansari/Documents/R/win-library/3.5/TCGAbiolinksGUI/app/server/elmer.R#357] 4: shiny::runApp 1: TCGAbiolinksGUI Warning: Error in gzfile: invalid 'description' argument 78: Warning: Error in gzfile: invalid 'description' argument 51: Warning: Error in gzfile: invalid 'description' argument 51:

I get this message.