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lloyd.izard
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80
@lloydizard-15069
Last seen 5.8 years ago
Good morning everyone,
I am just trying to deploy my app to https://www.shinyapps.io but as I do I get the following error :
Preparing to deploy application...DONE Uploading bundle for application: 305149...Detecting system locale ... DONE Deploying bundle: 1282230 for application: 305149 ... Waiting for task: 515286165 building: Processing bundle: 1282230 error: Parsing manifest ################################ Begin Task Log ################################ ################################# End Task Log ################################# Erreur : Unhandled Exception: Child Task 515286167 error: Unhandled Exception: Repository must be specified for Bioconductor package source De plus : Warning message: Error detecting locale: Error in read.table(file = file, header = header, sep = sep, quote = quote, : incomplete final line found by readTableHeader on 'raw' (Using default: en_US) Ex�cution arr�t�e
So the important error here is the following : Repository must be specified for Bioconductor package source
I went through all the forums I could but can't find a solution that is working for me.
I have tried to specify the location of my packages :
library(shiny, lib.loc="C:/Users/Lloyd/Documents/R/win-library/3.3") library(cluster, lib.loc="C:/Users/Lloyd/Documents/R/win-library/3.3") library(fpc, lib.loc="C:/Users/Lloyd/Documents/R/win-library/3.3") library(interactiveDisplay, lib.loc="C:/Users/Lloyd/Documents/R/win-library/3.3") library(flowCore, lib.loc="C:/Users/Lloyd/Documents/R/win-library/3.3")
but still, it doesn't work.
Here's some useful information:
> appDependencies() package version source 1 AnnotationDbi 1.40.0 Bioconductor 2 BH 1.66.0-1 CRAN 3 Biobase 2.38.0 Bioconductor 4 BiocGenerics 0.24.0 Bioconductor 5 Category 2.44.0 Bioconductor 6 DBI 0.8 CRAN 7 DEoptimR 1.0-8 CRAN 8 GSEABase 1.40.1 Bioconductor 9 IRanges 2.12.0 Bioconductor 10 MASS 7.3-49 CRAN 11 Matrix 1.2-12 CRAN 12 R6 2.2.2 CRAN 13 RBGL 1.54.0 Bioconductor 14 RColorBrewer 1.1-2 CRAN 15 RCurl 1.95-4.10 CRAN 16 RSQLite 2.0 CRAN 17 Rcpp 0.12.16 CRAN 18 S4Vectors 0.16.0 Bioconductor 19 XML 3.98-1.10 CRAN 20 annotate 1.56.1 Bioconductor 21 assertthat 0.2.0 CRAN 22 bit 1.1-12 CRAN 23 bit64 0.9-7 CRAN 24 bitops 1.0-6 CRAN 25 blob 1.1.0 CRAN 26 class 7.3-14 CRAN 27 cli 1.0.0 CRAN 28 cluster 2.0.6 CRAN 29 colorspace 1.3-2 CRAN 30 corpcor 1.6.9 CRAN 31 crayon 1.3.4 CRAN 32 dichromat 2.0-0 CRAN 33 digest 0.6.15 CRAN 34 diptest 0.75-7 CRAN 35 flexmix 2.3-14 CRAN 36 flowCore 1.44.2 Bioconductor 37 fpc 2.1-11 CRAN 38 genefilter 1.60.0 Bioconductor 39 ggplot2 2.2.1 CRAN 40 glue 1.2.0 CRAN 41 graph 1.56.0 Bioconductor 42 gridSVG 1.6-0 CRAN 43 gtable 0.2.0 CRAN 44 htmltools 0.3.6 CRAN 45 httpuv 1.3.6.2 CRAN 46 interactiveDisplay 1.16.0 Bioconductor 47 interactiveDisplayBase 1.16.0 Bioconductor 48 jsonlite 1.5 CRAN 49 kernlab 0.9-25 CRAN 50 labeling 0.3 CRAN 51 lattice 0.20-35 CRAN 52 lazyeval 0.2.1 CRAN 53 magrittr 1.5 CRAN 54 matrixStats 0.53.1 CRAN 55 mclust 5.4 CRAN 56 memoise 1.1.0 CRAN 57 mime 0.5 CRAN 58 modeltools 0.2-21 CRAN 59 munsell 0.4.3 CRAN 60 mvtnorm 1.0-7 CRAN 61 nnet 7.3-12 CRAN 62 packrat 0.4.9-1 CRAN 63 pcaPP 1.9-73 CRAN 64 pillar 1.2.1 CRAN 65 pkgconfig 2.0.1 CRAN 66 plogr 0.1-1 CRAN 67 plyr 1.8.4 CRAN 68 prabclus 2.2-6 CRAN 69 reshape2 1.4.3 CRAN 70 rlang 0.2.0 CRAN 71 robustbase 0.92-8 CRAN 72 rrcov 1.4-3 CRAN 73 scales 0.5.0 CRAN 74 shiny 1.0.5 CRAN 75 sourcetools 0.1.6 CRAN 76 stringi 1.1.7 CRAN 77 stringr 1.3.0 CRAN 78 survival 2.41-3 CRAN 79 tibble 1.4.2 CRAN 80 trimcluster 0.1-2 CRAN 81 utf8 1.1.3 CRAN 82 viridisLite 0.3.0 CRAN 83 xtable 1.8-2 CRAN > sessionInfo() R version 3.4.3 (2017-11-30) Platform: x86_64-w64-mingw32/x64 (64-bit) Running under: Windows 7 x64 (build 7601) Service Pack 1 Matrix products: default locale: [1] LC_COLLATE=French_France.1252 LC_CTYPE=French_France.1252 LC_MONETARY=French_France.1252 LC_NUMERIC=C [5] LC_TIME=French_France.1252 attached base packages: [1] stats graphics grDevices utils datasets methods base other attached packages: [1] shiny_1.0.5 rsconnect_0.8.8 loaded via a namespace (and not attached): [1] Rcpp_0.12.16 lattice_0.20-35 packrat_0.4.9-1 digest_0.6.15 mime_0.5 bitops_1.0-6 [7] grid_3.4.3 R6_2.2.2 xtable_1.8-2 BiocInstaller_1.28.0 Matrix_1.2-12 RJSONIO_1.3-0 [13] tools_3.4.3 RCurl_1.95-4.10 httpuv_1.3.6.2 yaml_2.1.18 compiler_3.4.3 htmltools_0.3.6
I'm blocked here guys, any help would be welcome.
Thanks a lot,
Lloyd
For anyone running into this error using the new BiocManager use:
Hi Lloyd,
Thanks for posting a solution!
Best regards,
Marcel