Input error - Githubissues

I am trying to run this app and am running into some trouble when i input the example data (exampleanalysisres_short.csv). My R Studio session just freezes. I am running it on a google chrome browser rather than the R-studio "browser", where it just kills it!

Since the file does not have p-vals, but rather adjp-vals, i am just using the same values from the files for both the inputs. Is this causing the freeze up?

Once i submit the files, it just greys over and i get a little "analyzing data .." Any help would be appreciated

Thanks

Error below: R version 3.5.1 (2018-07-02) Platform: x86_64-w64-mingw32/x64 (64-bit) Running under: Windows >= 8 x64 (build 9200)

Matrix products: default

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

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

other attached packages: [1] data.table_1.11.6 colourpicker_1.0 readr_1.1.1 heatmaply_0.15.2
[5] viridis_0.5.1 viridisLite_0.3.0 scales_1.0.0 NMF_0.21.0
[9] Biobase_2.40.0 BiocGenerics_0.26.0 cluster_2.0.7-1 rngtools_1.3.1
[13] pkgmaker_0.27 registry_0.5 markdown_0.8 plotly_4.8.0
[17] shinyBS_0.61 pheatmap_1.0.10 RColorBrewer_1.1-2 edgeR_3.22.4
[21] limma_3.36.5 DT_0.4 tidyr_0.8.1 dplyr_0.7.6
[25] ggvis_0.4.3 gplots_3.0.1 ggthemes_4.0.1 ggplot2_3.0.0
[29] reshape2_1.4.3 shiny_1.1.0

loaded via a namespace (and not attached): [1] bitops_1.0-6 webshot_0.5.0 doParallel_1.0.14 httr_1.3.1
[5] prabclus_2.2-6 tools_3.5.1 R6_2.2.2 KernSmooth_2.23-15
[9] lazyeval_0.2.1 colorspace_1.3-2 trimcluster_0.1-2.1 nnet_7.3-12
[13] withr_2.1.2 tidyselect_0.2.4 gridExtra_2.3 compiler_3.5.1
[17] TSP_1.1-6 diptest_0.75-7 caTools_1.17.1.1 DEoptimR_1.0-8
[21] mvtnorm_1.0-8 robustbase_0.93-3 stringr_1.3.1 digest_0.6.17
[25] pkgconfig_2.0.2 htmltools_0.3.6 bibtex_0.4.2 htmlwidgets_1.2
[29] rlang_0.2.2 rstudioapi_0.7 BiocInstaller_1.30.0 bindr_0.1.1
[33] jsonlite_1.5 crosstalk_1.0.0 mclust_5.4.1 gtools_3.8.1
[37] dendextend_1.8.0 magrittr_1.5 modeltools_0.2-22 Rcpp_0.12.18
[41] munsell_0.5.0 stringi_1.2.4 whisker_0.3-2 yaml_2.2.0
[45] MASS_7.3-50 flexmix_2.3-14 plyr_1.8.4 grid_3.5.1
[49] gdata_2.18.0 promises_1.0.1 crayon_1.3.4 miniUI_0.1.1.1
[53] lattice_0.20-35 hms_0.4.2 locfit_1.5-9.1 pillar_1.3.0
[57] fpc_2.1-11.1 codetools_0.2-15 stats4_3.5.1 glue_1.3.0
[61] gclus_1.3.1 httpuv_1.4.5 foreach_1.4.4 gtable_0.2.0
[65] purrr_0.2.5 kernlab_0.9-27 assertthat_0.2.0 gridBase_0.4-7
[69] mime_0.5 xtable_1.8-3 later_0.7.5 class_7.3-14
[73] seriation_1.2-3 tibble_1.4.2 iterators_1.0.10 bindrcpp_0.2.2
[1] "inputting data" Parsed with column specification: cols( Geneid = col_character(), MGIsymbol = col_character(), group1_1 = col_integer(), group1_2 = col_integer(), group1_3 = col_integer(), group2_1 = col_integer(), group2_2 = col_integer(), group2_3 = col_integer(), group3_1 = col_integer(), group3_2 = col_integer(), group3_3 = col_integer() ) [1] "uploaded mousecounts data" [1] "server-datafilter-update-filters" [1] "analysisCountDataReactive" [1] "server-datafilter-update-tests" [1] "server-datafilter-update-expr" [1] "server-dotplot-update" [1] "server-heatmap-update" [1] "server-samplegroupplots-update-yname" [1] "server-samplegroupplots-update-groups" [1] "server-sampleplots-update-samples" [1] "server-analysisres-update" [1] "drawing volcano plot" [1] "drawing scatterplot" [1] "inputting data" Parsed with column specification: cols( Geneid = col_character(), MGIsymbol = col_character(), group1_1 = col_integer(), group1_2 = col_integer(), group1_3 = col_integer(), group2_1 = col_integer(), group2_2 = col_integer(), group2_3 = col_integer(), group3_1 = col_integer(), group3_2 = col_integer(), group3_3 = col_integer() ) [1] "uploaded mousecounts data" [1] "server-datafilter-update-filters" [1] "analysisCountDataReactive" [1] "server-datafilter-update-tests" [1] "server-datafilter-update-expr" [1] "server-dotplot-update" [1] "server-heatmap-update" [1] "server-samplegroupplots-update-yname" [1] "server-samplegroupplots-update-groups" [1] "server-sampleplots-update-samples" [1] "server-analysisres-update" [1] "drawing volcano plot" [1] "drawing scatterplot" [1] "inputting data" [1] "server-datafilter-update-tests" [1] "server-datafilter-update-expr" [1] "server-sampleplots-update-samples" [1] "server-datafilter-update-tests" [1] "server-datafilter-update-expr" [1] "server-sampleplots-update-samples" [1] "updating analyzed data choices" [1] "inputting data" Parsed with column specification: cols( .default = col_double(), Geneid = col_character(), MGIsymbol = col_character() ) See spec(...) for full column specifications. [1] "uploaded seqdata" [1] "server-analysisres-update" [1] "analysisCountDataReactive" Warning in if (input == "") { : the condition has length > 1 and only the first element will be used [1] "Num genes kept after removing empty geneids: 100 of 100" Warning: Setting row names on a tibble is deprecated. Warning: Setting row names on a tibble is deprecated. Joining, by = c("unique_id", "test") Joining, by = c("unique_id", "test") Joining, by = "sampleid" Warning: Column sampleid joining character vector and factor, coercing into character vector [1] "drawing volcano plot" [1] "drawing scatterplot" [1] "server-datafilter-update-filters" [1] "server-datafilter-update-tests" Warning in max(tmpfc, na.rm = T) : no non-missing arguments to max; returning -Inf [1] "server-datafilter-update-expr" Warning: Error in FUN: only defined on a data frame with all numeric variables 50: stop 49: FUN 48: lapply 47: Summary.data.frame 46: [server-filterdata.R#77] 3: runApp 2: runUrl 1: shiny::runGitHub [1] "server-sampleplots-update-samples" [1] "server-dotplot-update" [1] "server-heatmap-update" [1] "server-samplegroupplots-update-yname" [1] "server-samplegroupplots-update-groups"

jminnier / STARTapp

Input error #6