Question

Found，但没有帮助。

我成功部署了一个应用程序，但是，在运行某些功能时出现错误。

我不确定出了什么问题。我加载了以下所需的R包：

# Packages requried
library(shiny)
library(markdown)
library(plyr)
library(data.table)
library(affy)
library(dplyr)
library(codelink)
library(simpleaffy)
library(lumi)
library(h20kcod.db)
library(h10kcod.db)
library(hwgcod.db)
library(limma)

和部署应用程序的会话：

Preparing to deploy application...DONE
Uploading bundle for application: 137665...DONE
Deploying bundle: 614851 for application: 137665 ...
Waiting for task: 295165350
  building: Processing bundle: 614851
  building: Parsing manifest
  building: Building image: 605478
  building: Fetching packages
  building: Installing packages
  building: Installing files
  building: Pushing image: 605478
  deploying: Starting instances
  success: Stopping old instances
Application successfully deployed
> rsconnect::showLogs()
2016-11-15T05:30:52.904308+00:00 shinyapps[137665]: Server version: 1.1.0-116
2016-11-15T05:30:52.904360+00:00 shinyapps[137665]: LANG: en_IN.UTF-8
2016-11-15T05:30:52.904396+00:00 shinyapps[137665]: R version: 3.3.2
2016-11-15T05:30:52.904399+00:00 shinyapps[137665]: shiny version: 0.14.2
2016-11-15T05:30:52.904399+00:00 shinyapps[137665]: rmarkdown version: NA
2016-11-15T05:30:52.904400+00:00 shinyapps[137665]: knitr version: NA
2016-11-15T05:30:52.904421+00:00 shinyapps[137665]: jsonlite version: 1.1
2016-11-15T05:30:52.904422+00:00 shinyapps[137665]: RJSONIO version: NA
2016-11-15T05:30:52.904422+00:00 shinyapps[137665]: htmltools version: 0.3.5
2016-11-15T05:30:53.112438+00:00 shinyapps[137665]: Using jsonlite for JSON processing
2016-11-15T05:30:53.116924+00:00 shinyapps[137665]: 
2016-11-15T05:30:53.136581+00:00 shinyapps[137665]: Listening on http://0.0.0.0:46164
2016-11-15T05:30:53.116929+00:00 shinyapps[137665]: Starting R with process ID: '16'
2016-11-15T05:30:53.136579+00:00 shinyapps[137665]:

我认为像codelink, simpleaffy, lumi, h20kcod.db, h10kcod.db, hwgcod.db, limma这样的生物传感器包有问题，但是无法解决。

更新：（11月12日）找到以下会话日志，并显示警告和错误消息

2016-11-16T06:36:10.792579+00:00 shinyapps[137665]: background correction: mas 
2016-11-16T06:36:10.792602+00:00 shinyapps[137665]: PM/MM correction : mas 
2016-11-16T06:36:10.792604+00:00 shinyapps[137665]: expression values: mas 
2016-11-16T06:36:12.487215+00:00 shinyapps[137665]: background correcting...Warning in install.packages(cdfname, lib = lib, repos = biocinstallRepos(),  :
2016-11-16T06:36:12.487219+00:00 shinyapps[137665]:   'lib = "/usr/local/lib/R/site-library"' is not writable
2016-11-16T06:36:12.490008+00:00 shinyapps[137665]: Warning: Error in install.packages: unable to install packages
2016-11-16T06:36:12.497285+00:00 shinyapps[137665]: Stack trace (innermost first):
2016-11-16T06:36:12.497286+00:00 shinyapps[137665]:     133: install.packages
2016-11-16T06:36:12.497287+00:00 shinyapps[137665]:     132: cdfFromBioC
2016-11-16T06:36:12.497287+00:00 shinyapps[137665]:     131: getCdfInfo
2016-11-16T06:36:12.497288+00:00 shinyapps[137665]:     130: .local
2016-11-16T06:36:12.497288+00:00 shinyapps[137665]:     129: indexProbes
2016-11-16T06:36:12.497289+00:00 shinyapps[137665]:     128: indexProbes
2016-11-16T06:36:12.497289+00:00 shinyapps[137665]:     127: unlist
2016-11-16T06:36:12.497289+00:00 shinyapps[137665]:     126: unique
2016-11-16T06:36:12.497290+00:00 shinyapps[137665]:     125: bg.correct.mas
2016-11-16T06:36:12.497290+00:00 shinyapps[137665]:     124: do.call
2016-11-16T06:36:12.497291+00:00 shinyapps[137665]:     123: <Anonymous>
2016-11-16T06:36:12.497291+00:00 shinyapps[137665]:     122: <Anonymous>
2016-11-16T06:36:12.497291+00:00 shinyapps[137665]:     121: do.call
2016-11-16T06:36:12.497292+00:00 shinyapps[137665]:     120: expresso
2016-11-16T06:36:12.497292+00:00 shinyapps[137665]:     119: mas5
2016-11-16T06:36:12.497293+00:00 shinyapps[137665]:     118: processed_data [/srv/connect/apps/mamged/server.r#95]
2016-11-16T06:36:12.497293+00:00 shinyapps[137665]:     117: eval [/srv/connect/apps/mamged/server.r#1240]
2016-11-16T06:36:12.497293+00:00 shinyapps[137665]:     116: eval
2016-11-16T06:36:12.497294+00:00 shinyapps[137665]:     115: withProgress
2016-11-16T06:36:12.497294+00:00 shinyapps[137665]:     114: eventReactiveHandler [/srv/connect/apps/mamged/server.r#1227]
2016-11-16T06:36:12.497295+00:00 shinyapps[137665]:      94: list_files
2016-11-16T06:36:12.497295+00:00 shinyapps[137665]:      93: renderDataTable [/srv/connect/apps/mamged/server.r#1545]
2016-11-16T06:36:12.497295+00:00 shinyapps[137665]:      92: func
2016-11-16T06:36:12.497296+00:00 shinyapps[137665]:      91: origRenderFunc
2016-11-16T06:36:12.497296+00:00 shinyapps[137665]:      90: output$sourced
2016-11-16T06:36:12.497296+00:00 shinyapps[137665]:      13: runApp
2016-11-16T06:36:12.497297+00:00 shinyapps[137665]:      12: fn
2016-11-16T06:36:12.497297+00:00 shinyapps[137665]:      11: doTryCatch
2016-11-16T06:36:12.497297+00:00 shinyapps[137665]:      10: tryCatchOne
2016-11-16T06:36:12.497297+00:00 shinyapps[137665]:       9: tryCatchList
2016-11-16T06:36:12.497298+00:00 shinyapps[137665]:       8: tryCatch
2016-11-16T06:36:12.497298+00:00 shinyapps[137665]:       7: connect$retry
2016-11-16T06:36:12.497298+00:00 shinyapps[137665]:       6: eval
2016-11-16T06:36:12.497299+00:00 shinyapps[137665]:       5: eval
2016-11-16T06:36:12.497299+00:00 shinyapps[137665]:       4: eval
2016-11-16T06:36:12.497299+00:00 shinyapps[137665]:       3: eval
2016-11-16T06:36:12.497299+00:00 shinyapps[137665]:       2: eval.parent
2016-11-16T06:36:12.497300+00:00 shinyapps[137665]:       1: local

更多更新（11月17日）未附加affy R包，如以下会话日志中所示。 affy功能不起作用。这是问题??

ioconductor version 3.4 (BiocInstaller 1.24.0), ?biocLite for help
2016-11-17T10:50:13.361491+00:00 shinyapps[137665]: Loading required package: BiocGenerics
2016-11-17T10:50:13.365265+00:00 shinyapps[137665]: Loading required package: parallel
2016-11-17T10:50:13.525417+00:00 shinyapps[137665]: 
2016-11-17T10:50:13.525421+00:00 shinyapps[137665]: Attaching package: ‘BiocGenerics’
2016-11-17T10:50:13.525421+00:00 shinyapps[137665]: 
2016-11-17T10:50:13.525975+00:00 shinyapps[137665]: The following objects are masked from ‘package:parallel’:
2016-11-17T10:50:13.525977+00:00 shinyapps[137665]: 
2016-11-17T10:50:13.525977+00:00 shinyapps[137665]:     clusterApply, clusterApplyLB, clusterCall, clusterEvalQ,
2016-11-17T10:50:13.525978+00:00 shinyapps[137665]:     clusterExport, clusterMap, parApply, parCapply, parLapply,
2016-11-17T10:50:13.525978+00:00 shinyapps[137665]:     parLapplyLB, parRapply, parSapply, parSapplyLB
2016-11-17T10:50:13.525978+00:00 shinyapps[137665]: 
2016-11-17T10:50:13.526948+00:00 shinyapps[137665]: The following objects are masked from ‘package:stats’:
2016-11-17T10:50:13.526950+00:00 shinyapps[137665]: 
2016-11-17T10:50:13.526951+00:00 shinyapps[137665]:     IQR, mad, xtabs
2016-11-17T10:50:13.526951+00:00 shinyapps[137665]: 
2016-11-17T10:50:13.530404+00:00 shinyapps[137665]: The following objects are masked from ‘package:base’:
2016-11-17T10:50:13.530406+00:00 shinyapps[137665]: 
2016-11-17T10:50:13.530407+00:00 shinyapps[137665]:     anyDuplicated, append, as.data.frame, cbind, colnames, do.call,
2016-11-17T10:50:13.530407+00:00 shinyapps[137665]:     duplicated, eval, evalq, Filter, Find, get, grep, grepl, intersect,
2016-11-17T10:50:13.530407+00:00 shinyapps[137665]:     is.unsorted, lapply, lengths, Map, mapply, match, mget, order,
2016-11-17T10:50:13.530408+00:00 shinyapps[137665]:     paste, pmax, pmax.int, pmin, pmin.int, Position, rank, rbind,
2016-11-17T10:50:13.530408+00:00 shinyapps[137665]:     Reduce, rownames, sapply, setdiff, sort, table, tapply, union,
2016-11-17T10:50:13.530409+00:00 shinyapps[137665]:     unique, unsplit, which, which.max, which.min
2016-11-17T10:50:13.530409+00:00 shinyapps[137665]: 
2016-11-17T10:50:13.781403+00:00 shinyapps[137665]: Welcome to Bioconductor
2016-11-17T10:50:13.781406+00:00 shinyapps[137665]: 
2016-11-17T10:50:13.781407+00:00 shinyapps[137665]:     Vignettes contain introductory material; view with
2016-11-17T10:50:13.781407+00:00 shinyapps[137665]:     'browseVignettes()'. To cite Bioconductor, see
2016-11-17T10:50:13.781408+00:00 shinyapps[137665]:     'citation("Biobase")', and for packages 'citation("pkgname")'.
2016-11-17T10:50:13.781408+00:00 shinyapps[137665]: 
2016-11-17T10:50:15.902935+00:00 shinyapps[137665]: Loading required package: S4Vectors
2016-11-17T10:50:15.906891+00:00 shinyapps[137665]: Loading required package: stats4
2016-11-17T10:50:15.917693+00:00 shinyapps[137665]: 
2016-11-17T10:50:15.917695+00:00 shinyapps[137665]: Attaching package: ‘S4Vectors’
2016-11-17T10:50:15.917696+00:00 shinyapps[137665]: 
2016-11-17T10:50:15.918150+00:00 shinyapps[137665]: The following objects are masked from ‘package:base’:
2016-11-17T10:50:15.918151+00:00 shinyapps[137665]: 
2016-11-17T10:50:15.918152+00:00 shinyapps[137665]:     colMeans, colSums, expand.grid, rowMeans, rowSums
2016-11-17T10:50:15.918152+00:00 shinyapps[137665]: 
2016-11-17T10:50:15.919567+00:00 shinyapps[137665]: Loading required package: IRanges
2016-11-17T10:50:15.931953+00:00 shinyapps[137665]: Loading required package: XVector
2016-11-17T10:50:17.806882+00:00 shinyapps[137665]: Warning: replacing previous import ‘AnnotationDbi::tail’ by ‘utils::tail’ when loading ‘hgu133plus2cdf’
2016-11-17T10:50:17.807394+00:00 shinyapps[137665]: Warning: replacing previous import ‘AnnotationDbi::head’ by ‘utils::head’ when loading ‘hgu133plus2cdf’
2016-11-17T10:50:18.124280+00:00 shinyapps[137665]: 
2016-11-17T10:50:18.274247+00:00 shinyapps[137665]: 
2016-11-17T10:50:18.274251+00:00 shinyapps[137665]: Attaching package: ‘plyr’
2016-11-17T10:50:18.274251+00:00 shinyapps[137665]: 
2016-11-17T10:50:18.274841+00:00 shinyapps[137665]: The following object is masked from ‘package:XVector’:
2016-11-17T10:50:18.274843+00:00 shinyapps[137665]: 
2016-11-17T10:50:18.274844+00:00 shinyapps[137665]:     compact
2016-11-17T10:50:18.274844+00:00 shinyapps[137665]: 
2016-11-17T10:50:18.275576+00:00 shinyapps[137665]: The following object is masked from ‘package:IRanges’:
2016-11-17T10:50:18.275578+00:00 shinyapps[137665]: 
2016-11-17T10:50:18.275579+00:00 shinyapps[137665]:     desc
2016-11-17T10:50:18.275579+00:00 shinyapps[137665]: 
2016-11-17T10:50:18.276316+00:00 shinyapps[137665]: The following object is masked from ‘package:S4Vectors’:
2016-11-17T10:50:18.276318+00:00 shinyapps[137665]: 
2016-11-17T10:50:18.276318+00:00 shinyapps[137665]:     rename
2016-11-17T10:50:18.276318+00:00 shinyapps[137665]: 
2016-11-17T10:50:18.490843+00:00 shinyapps[137665]: 
2016-11-17T10:50:18.490846+00:00 shinyapps[137665]: Attaching package: ‘data.table’
2016-11-17T10:50:18.490848+00:00 shinyapps[137665]: 
2016-11-17T10:50:18.491422+00:00 shinyapps[137665]: The following object is masked from ‘package:IRanges’:
2016-11-17T10:50:18.491424+00:00 shinyapps[137665]: 
2016-11-17T10:50:18.491425+00:00 shinyapps[137665]:     shift
2016-11-17T10:50:18.491426+00:00 shinyapps[137665]: 
2016-11-17T10:50:18.935983+00:00 shinyapps[137665]: ------------------------------------------------------------------------------
2016-11-17T10:50:18.936424+00:00 shinyapps[137665]: data.table + dplyr code now lives in dtplyr.
2016-11-17T10:50:18.936427+00:00 shinyapps[137665]: Please library(dtplyr)!
2016-11-17T10:50:18.936907+00:00 shinyapps[137665]: ------------------------------------------------------------------------------
2016-11-17T10:50:18.938105+00:00 shinyapps[137665]: 
2016-11-17T10:50:18.938106+00:00 shinyapps[137665]: Attaching package: ‘dplyr’
2016-11-17T10:50:18.938106+00:00 shinyapps[137665]: 
2016-11-17T10:50:18.938728+00:00 shinyapps[137665]: The following objects are masked from ‘package:data.table’:
2016-11-17T10:50:18.938729+00:00 shinyapps[137665]: 
2016-11-17T10:50:18.938730+00:00 shinyapps[137665]:     between, last
2016-11-17T10:50:18.938730+00:00 shinyapps[137665]: 
2016-11-17T10:50:18.940386+00:00 shinyapps[137665]: The following objects are masked from ‘package:plyr’:
2016-11-17T10:50:18.940387+00:00 shinyapps[137665]: 
2016-11-17T10:50:18.940388+00:00 shinyapps[137665]:     arrange, count, desc, failwith, id, mutate, rename, summarise,
2016-11-17T10:50:18.940388+00:00 shinyapps[137665]:     summarize
2016-11-17T10:50:18.940389+00:00 shinyapps[137665]: 
2016-11-17T10:50:18.941386+00:00 shinyapps[137665]: The following objects are masked from ‘package:Biostrings’:
2016-11-17T10:50:18.941387+00:00 shinyapps[137665]: 
2016-11-17T10:50:18.941388+00:00 shinyapps[137665]:     collapse, intersect, setdiff, setequal, union
2016-11-17T10:50:18.941388+00:00 shinyapps[137665]: 
2016-11-17T10:50:18.942071+00:00 shinyapps[137665]: The following object is masked from ‘package:XVector’:
2016-11-17T10:50:18.942072+00:00 shinyapps[137665]: 
2016-11-17T10:50:18.942073+00:00 shinyapps[137665]:     slice
2016-11-17T10:50:18.942073+00:00 shinyapps[137665]: 
2016-11-17T10:50:18.943024+00:00 shinyapps[137665]: The following objects are masked from ‘package:IRanges’:
2016-11-17T10:50:18.943025+00:00 shinyapps[137665]: 
2016-11-17T10:50:18.943025+00:00 shinyapps[137665]:     collapse, desc, intersect, regroup, setdiff, slice, union
2016-11-17T10:50:18.943026+00:00 shinyapps[137665]: 
2016-11-17T10:50:18.943856+00:00 shinyapps[137665]: The following objects are masked from ‘package:S4Vectors’:
2016-11-17T10:50:18.943857+00:00 shinyapps[137665]: 
2016-11-17T10:50:18.943858+00:00 shinyapps[137665]:     first, intersect, rename, setdiff, setequal, union
2016-11-17T10:50:18.943858+00:00 shinyapps[137665]: 
2016-11-17T10:50:18.944534+00:00 shinyapps[137665]: The following object is masked from ‘package:biomaRt’:
2016-11-17T10:50:18.944535+00:00 shinyapps[137665]: 
2016-11-17T10:50:18.944535+00:00 shinyapps[137665]:     select
2016-11-17T10:50:18.944536+00:00 shinyapps[137665]: 
2016-11-17T10:50:18.945358+00:00 shinyapps[137665]: The following object is masked from ‘package:Biobase’:
2016-11-17T10:50:18.945359+00:00 shinyapps[137665]: 
2016-11-17T10:50:18.945360+00:00 shinyapps[137665]:     combine
2016-11-17T10:50:18.945360+00:00 shinyapps[137665]: 
2016-11-17T10:50:18.946102+00:00 shinyapps[137665]: The following objects are masked from ‘package:BiocGenerics’:
2016-11-17T10:50:18.946103+00:00 shinyapps[137665]: 
2016-11-17T10:50:18.946104+00:00 shinyapps[137665]:     combine, intersect, setdiff, union
2016-11-17T10:50:18.946104+00:00 shinyapps[137665]: 
2016-11-17T10:50:18.947248+00:00 shinyapps[137665]: The following objects are masked from ‘package:stats’:
2016-11-17T10:50:18.947249+00:00 shinyapps[137665]: 
2016-11-17T10:50:18.947250+00:00 shinyapps[137665]:     filter, lag
2016-11-17T10:50:18.947250+00:00 shinyapps[137665]: 
2016-11-17T10:50:18.955856+00:00 shinyapps[137665]: The following objects are masked from ‘package:base’:
2016-11-17T10:50:18.955857+00:00 shinyapps[137665]: 
2016-11-17T10:50:18.955858+00:00 shinyapps[137665]:     intersect, setdiff, setequal, union
2016-11-17T10:50:18.955860+00:00 shinyapps[137665]: 
2016-11-17T10:50:18.963064+00:00 shinyapps[137665]: Loading required package: limma
2016-11-17T10:50:19.193374+00:00 shinyapps[137665]: 
2016-11-17T10:50:19.193376+00:00 shinyapps[137665]: Attaching package: ‘limma’
2016-11-17T10:50:19.193377+00:00 shinyapps[137665]: 
2016-11-17T10:50:19.193969+00:00 shinyapps[137665]: The following object is masked from ‘package:BiocGenerics’:
2016-11-17T10:50:19.193972+00:00 shinyapps[137665]: 
2016-11-17T10:50:19.193972+00:00 shinyapps[137665]:     plotMA
2016-11-17T10:50:19.193972+00:00 shinyapps[137665]: 
2016-11-17T10:50:19.316770+00:00 shinyapps[137665]: 
2016-11-17T10:50:19.316774+00:00 shinyapps[137665]: Attaching package: ‘codelink’
2016-11-17T10:50:19.316775+00:00 shinyapps[137665]: 
2016-11-17T10:50:19.317440+00:00 shinyapps[137665]: The following objects are masked from ‘package:limma’:
2016-11-17T10:50:19.317443+00:00 shinyapps[137665]: 
2016-11-17T10:50:19.317444+00:00 shinyapps[137665]:     plotDensities, plotMA
2016-11-17T10:50:19.317444+00:00 shinyapps[137665]: 
2016-11-17T10:50:19.318205+00:00 shinyapps[137665]: The following object is masked from ‘package:affy’:
2016-11-17T10:50:19.318207+00:00 shinyapps[137665]: 
2016-11-17T10:50:19.318208+00:00 shinyapps[137665]:     probeNames
2016-11-17T10:50:19.318208+00:00 shinyapps[137665]: 
2016-11-17T10:50:19.319400+00:00 shinyapps[137665]: The following object is masked from ‘package:BiocGenerics’:
2016-11-17T10:50:19.319402+00:00 shinyapps[137665]: 
2016-11-17T10:50:19.319402+00:00 shinyapps[137665]:     plotMA
2016-11-17T10:50:19.319403+00:00 shinyapps[137665]: 
2016-11-17T10:50:23.173170+00:00 shinyapps[137665]: Setting options('download.file.method.GEOquery'='auto')
2016-11-17T10:50:23.173692+00:00 shinyapps[137665]: Setting options('GEOquery.inmemory.gpl'=FALSE)
2016-11-17T10:50:23.702856+00:00 shinyapps[137665]: 
2016-11-17T10:50:23.702861+00:00 shinyapps[137665]: Attaching package: ‘lumi’
2016-11-17T10:50:23.702863+00:00 shinyapps[137665]: 
2016-11-17T10:50:23.703506+00:00 shinyapps[137665]: The following objects are masked from ‘package:affy’:
2016-11-17T10:50:23.703508+00:00 shinyapps[137665]: 
2016-11-17T10:50:23.703509+00:00 shinyapps[137665]:     MAplot, plotDensity
2016-11-17T10:50:23.703509+00:00 shinyapps[137665]: 
2016-11-17T10:50:23.715921+00:00 shinyapps[137665]: Loading required package: AnnotationDbi
2016-11-17T10:50:23.733821+00:00 shinyapps[137665]: 
2016-11-17T10:50:23.733822+00:00 shinyapps[137665]: Attaching package: ‘AnnotationDbi’
2016-11-17T10:50:23.733823+00:00 shinyapps[137665]: 
2016-11-17T10:50:23.734434+00:00 shinyapps[137665]: The following object is masked from ‘package:dplyr’:
2016-11-17T10:50:23.734435+00:00 shinyapps[137665]: 
2016-11-17T10:50:23.734436+00:00 shinyapps[137665]:     select
2016-11-17T10:50:23.734437+00:00 shinyapps[137665]: 
2016-11-17T10:50:23.743475+00:00 shinyapps[137665]: Loading required package: org.Hs.eg.db
2016-11-17T10:50:23.876778+00:00 shinyapps[137665]: 
2016-11-17T10:50:24.005934+00:00 shinyapps[137665]: 
2016-11-17T10:50:24.091956+00:00 shinyapps[137665]: 
2016-11-17T10:50:24.205034+00:00 shinyapps[137665]: 
2016-11-17T10:50:24.472464+00:00 shinyapps[137665]:

错误：无法在闪亮的应用程序中安装软件包

0 个答案: