Error when deploying shiny application to shinyapp.io
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yuanhang liu
Sep 16, 2016, 3:14:26 PM9/16/16
to shinyapps.io Users
Hello, everyone,
I don't see anything particularly wrong. I tried deleting rsconnect folder and deploy again as suggested by Alper Kucukural. But it didn't work. Any help would be appreciated!
I encountered one issue when trying to deploying my shiny application to shinyapp.io. The error message is 'Unhandled Exception: Repository must be specified for Bioconductor package source'.
The output to appDenpedencies():
package version source1 AnnotationDbi 1.34.4 Bioconductor2 BH 1.60.0-2 CRAN3 BPSC 0.99.0 github4 Biobase 2.32.0 Bioconductor5 BiocGenerics 0.18.0 Bioconductor6 BiocParallel 1.6.6 Bioconductor7 Biostrings 2.40.2 Bioconductor8 Cairo 1.5-9 CRAN9 DBI 0.5-1 CRAN10 DESeq 1.24.0 Bioconductor11 DESeq2 1.12.4 Bioconductor12 DEoptimR 1.0-6 CRAN13 DT 0.2 CRAN14 Delaporte 3.0.0 CRAN15 EBSeq 1.12.0 Bioconductor16 EDASeq 2.6.2 Bioconductor17 Formula 1.2-1 CRAN18 GGally 1.2.0 CRAN19 GenomeInfoDb 1.8.7 Bioconductor20 GenomicAlignments 1.8.4 Bioconductor21 GenomicFeatures 1.24.5 Bioconductor22 GenomicRanges 1.24.3 Bioconductor23 HSMMSingleCell 0.106.2 Bioconductor24 Hmisc 3.17-4 CRAN25 IRanges 2.6.1 Bioconductor26 KernSmooth 2.23-15 CRAN27 LPCM 0.45-0 CRAN28 Lmoments 1.2-3 CRAN29 MASS 7.3-45 CRAN30 MAST 0.934 github31 Matrix 1.2-7.1 CRAN32 MatrixModels 0.4-1 CRAN33 NMF 0.20.6 CRAN34 NetSAM 1.12.0 Bioconductor35 R.methodsS3 1.7.1 CRAN36 R.oo 1.20.0 CRAN37 R.utils 2.4.0 CRAN38 R6 2.1.3 CRAN39 RColorBrewer 1.1-2 CRAN40 RCurl 1.95-4.8 CRAN41 RJSONIO 1.3-0 CRAN42 RMTstat 0.3 CRAN43 ROTS 1.0.0 Bioconductor44 RSQLite 1.0.0 CRAN45 RUVSeq 1.6.2 Bioconductor46 Rcpp 0.12.7 CRAN47 RcppArmadillo 0.7.400.2.0 CRAN48 RcppEigen 0.3.2.9.0 CRAN49 Rook 1.1-1 CRAN50 Rsamtools 1.24.0 Bioconductor51 S4Vectors 0.10.3 Bioconductor52 ShortRead 1.30.0 Bioconductor53 SparseM 1.72 CRAN54 SummarizedExperiment 1.2.3 Bioconductor55 TSP 1.1-4 CRAN56 VGAM 1.0-2 CRAN57 XBSeq 1.2.2 Bioconductor58 XML 3.98-1.4 CRAN59 XVector 0.12.1 Bioconductor60 abind 1.4-5 CRAN61 acepack 1.3-3.3 CRAN62 annotate 1.50.0 Bioconductor63 aroma.light 3.2.0 Bioconductor64 assertthat 0.1 CRAN65 base64enc 0.1-3 CRAN66 biomaRt 2.28.0 Bioconductor67 bitops 1.0-6 CRAN68 blockmodeling 0.1.8 CRAN69 brew 1.0-6 CRAN70 caTools 1.17.1 CRAN71 car 2.1-3 CRAN72 chron 2.3-47 CRAN73 class 7.3-14 CRAN74 cluster 2.0.4 CRAN75 codetools 0.2-14 CRAN76 colorspace 1.2-6 CRAN77 combinat 0.0-8 CRAN78 crayon 1.3.2 CRAN79 curl 1.2 CRAN80 d3heatmap 0.6.1.1 CRAN81 data.table 1.9.6 CRAN82 dendextend 1.3.0 CRAN83 dichromat 2.0-0 CRAN84 digest 0.6.10 CRAN85 diptest 0.75-7 CRAN86 distillery 1.0-2 CRAN87 doParallel 1.0.10 CRAN88 dplyr 0.5.0 CRAN89 edgeR 3.14.0 Bioconductor90 evaluate 0.9 CRAN91 extRemes 2.0-8 CRAN92 fastICA 1.2-0 CRAN93 flexmix 2.3-13 CRAN94 foreach 1.4.3 CRAN95 foreign 0.8-67 CRAN96 formatR 1.4 CRAN97 fpc 2.1-10 CRAN98 futile.logger 1.4.3 CRAN99 futile.options 1.0.0 CRAN100 gclus 1.3.1 CRAN101 gdata 2.17.0 CRAN102 genefilter 1.54.2 Bioconductor103 geneplotter 1.50.0 Bioconductor104 ggplot2 2.1.0 CRAN105 gplots 3.0.1 CRAN106 graph 1.50.0 Bioconductor107 gridBase 0.4-7 CRAN108 gridExtra 2.2.1 CRAN109 gtable 0.2.0 CRAN110 gtools 3.5.0 CRAN111 highr 0.6 CRAN112 htmltools 0.3.5 CRAN113 htmlwidgets 0.7 CRAN114 httpuv 1.3.3 CRAN115 httr 1.2.1 CRAN116 hwriter 1.3.2 CRAN117 igraph 1.0.1 CRAN118 irlba 2.1.1 CRAN119 iterators 1.0.8 CRAN120 jsonlite 1.1 CRAN121 kernlab 0.9-24 CRAN122 knitr 1.14 CRAN123 labeling 0.3 CRAN124 lambda.r 1.1.9 CRAN125 lattice 0.20-34 CRAN126 latticeExtra 0.6-28 CRAN127 lazyeval 0.2.0 CRAN128 limma 3.28.21 Bioconductor129 lme4 1.1-12 CRAN130 locfit 1.5-9.1 CRAN131 magrittr 1.5 CRAN132 markdown 0.7.7 CRAN133 matrixStats 0.50.2 Bioconductor134 mclust 5.2 CRAN135 metricsgraphics 0.9.0 CRAN136 mgcv 1.8-15 CRAN137 mime 0.5 CRAN138 minqa 1.2.4 CRAN139 modeltools 0.2-21 CRAN140 monocle 1.6.2 Bioconductor141 munsell 0.4.3 CRAN142 mvtnorm 1.0-5 CRAN143 networkD3 0.2.13 CRAN144 nlme 3.1-128 CRAN145 nloptr 1.0.4 CRAN146 nnet 7.3-12 CRAN147 openssl 0.9.4 CRAN148 packrat 0.4.8-1 CRAN149 pbkrtest 0.4-6 CRAN150 pcaMethods 1.64.0 Bioconductor151 pkgmaker 0.22 CRAN152 plyr 1.8.4 CRAN153 png 0.1-7 CRAN154 prabclus 2.2-6 CRAN155 pracma 1.9.5 CRAN156 praise 1.0.0 CRAN157 preprocessCore 1.34.0 Bioconductor158 qap 0.1-0 CRAN159 quadprog 1.5-5 CRAN160 quantreg 5.29 CRAN161 rCharts 0.4.5 github162 registry 0.3 CRAN163 reshape 0.8.5 CRAN164 reshape2 1.4.1 CRAN165 rga 0.8 github166 rjson 0.2.15 CRAN167 rmarkdown 1.0 CRAN168 rngtools 1.2.4 CRAN169 robustbase 0.92-6 CRAN170 rpart 4.1-10 CRAN171 rtracklayer 1.32.2 Bioconductor172 scales 0.4.0 CRAN173 scatterplot3d 0.3-37 CRAN174 scde 2.0.1 Bioconductor175 seriation 1.2-1 CRAN176 shiny 0.14 CRAN177 shinydashboard 0.5.2 CRAN178 shinythemes 1.0.1 CRAN179 slidify 0.5 github180 slidifyLibraries 0.3.1 github181 snow 0.4-1 CRAN182 sourcetools 0.1.5 CRAN183 statmod 1.4.26 CRAN184 stringi 1.1.1 CRAN185 stringr 1.1.0 CRAN186 survival 2.39-5 CRAN187 testthat 1.0.2 CRAN188 threejs 0.2.2 CRAN189 tibble 1.2 CRAN190 trimcluster 0.1-2 CRAN191 whisker 0.3-2 CRAN192 xtable 1.8-2 CRAN193 yaml 2.1.13 CRAN194 zlibbioc 1.18.0 BioconductorI don't see anything particularly wrong. I tried deleting rsconnect folder and deploy again as suggested by Alper Kucukural. But it didn't work. Any help would be appreciated!
yuanhang liu
Sep 20, 2016, 5:32:42 PM9/20/16
to shinyapps.io Users
Tried uninstall and reinstall all the Bioconductor packages, but still without any luck.
Leon Shi
Sep 20, 2016, 10:25:18 PM9/20/16
to shinyapps.io Users
Hi, Yuanhang,
在 2016年9月17日星期六 UTC+8上午3:14:26，yuanhang liu写道：
I came across the same problem these days when deploying my shinyapp and found no online solution anywhere. Thus, I debugged the problem step by step and finally got the answer. The failure of deployment, at least in my situation, was caused from the inconsistent sources of one dependency package: "matrixStats". I noticed that this package also appeared in your appDependencies, which confirmed my hypothesis.
In detail, the package "matrixStats" is a "CRAN" package, which means it can be found and installed from CRAN. However, in the output of the function "appDependencies()", you can find that the source of "matrixStats" is "Bioconductor". Some packages could be found both in CRAN and Bioconductor, but unfortunately, "matrixStats" is not one of them. I don't know why "appDependencies()" detected the wrong source, and also I didn't go deep into this problem. I guess this might be a bug of the function "appDependencies()".
My solution to the problem is to re-install the package "matrixStats" from Github. Go to the CRAN page of "matrixStats" and you can find the URL. You may need to install Rtools first, and then using
to finish re-installation. This can change some properties of the package. Now, when you "appDependencies()" again, you can find that the source of "matrixStats" has changed into "github". I deployed my shinyapp successfully after that.
devtools::install_github("HenrikBengtsson/matrixStats")to finish re-installation. This can change some properties of the package. Now, when you "appDependencies()" again, you can find that the source of "matrixStats" has changed into "github". I deployed my shinyapp successfully after that.
Hope my finding and solution are helpful to you. Good luck~
Leon
在 2016年9月17日星期六 UTC+8上午3:14:26，yuanhang liu写道：
yuanhang liu
Sep 26, 2016, 12:38:28 PM9/26/16
to shinyapps.io Users
Hi, Dear, Leon,
Thanks so much for your advice. It solved my problem perfectly. Thanks again for your help!
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