闪亮的服务器发生错误加载命名空间时没有软件包rcpp，但是安装了rcpp并在R中加载了闪亮的作品

Question

I was recently trying to open a shiny server app on my server and got this error which I have never seen before.

   Error in loadNamespace(j <- i[[1L]], c(lib.loc, .libPaths()), versionCheck     = vI[[j]]) : 
      there is no package called ‘Rcpp’
    Error: package or namespace load failed for ‘shiny’
    Execution halted

I am assuming an update broke something. However when starting R on my machine both library(shiny) as well as library(Rcpp) load without any issues.

So I tried re-installing shiny-server. According to their instructions here , however I basically get the same error as above:

sudo su - \
> -c "R -e \"install.packages('shiny', repos='http://cran.rstudio.com/')\""

R version 3.2.1 (2015-06-18) -- "World-Famous Astronaut"
Copyright (C) 2015 The R Foundation for Statistical Computing
Platform: x86_64-pc-linux-gnu (64-bit)

R is free software and comes with ABSOLUTELY NO WARRANTY.
You are welcome to redistribute it under certain conditions.
Type 'license()' or 'licence()' for distribution details.

  Natural language support but running in an English locale

R is a collaborative project with many contributors.
Type 'contributors()' for more information and
'citation()' on how to cite R or R packages in publications.

Type 'demo()' for some demos, 'help()' for on-line help, or
'help.start()' for an HTML browser interface to help.
Type 'q()' to quit R.

> install.packages('shiny', repos='http://cran.rstudio.com/')
Installing package into â/usr/local/lib/R/site-libraryâ
(as âlibâ is unspecified)
trying URL 'http://cran.rstudio.com/src/contrib/shiny_0.12.1.tar.gz'
Content type 'application/x-gzip' length 1473559 bytes (1.4 MB)
==================================================
downloaded 1.4 MB

* installing *source* package âshinyâ ...
** package âshinyâ successfully unpacked and MD5 sums checked
** R
** inst
** preparing package for lazy loading
Error in loadNamespace(j <- i[[1L]], c(lib.loc, .libPaths()), versionCheck = vI[[j]]) :
  there is no package called âRcppâ
ERROR: lazy loading failed for package âshinyâ
* removing â/usr/local/lib/R/site-library/shinyâ
* restoring previous â/usr/local/lib/R/site-library/shinyâ

The downloaded source packages are in
        â/tmp/RtmpUfc19u/downloaded_packagesâ
Warning message:
In install.packages("shiny", repos = "http://cran.rstudio.com/") :
  installation of package âshinyâ had non-zero exit status

I have no idea why this is, since both shiny and Rcpp install and load flawlessy when just starting R or even when starting R as sudo.

My sessionInfo() output is:

R version 3.2.1 (2015-06-18)
Platform: x86_64-pc-linux-gnu (64-bit)
Running under: Ubuntu precise (12.04.5 LTS)

locale:
 [1] LC_CTYPE=en_US.UTF-8       LC_NUMERIC=C
 [3] LC_TIME=en_US.UTF-8        LC_COLLATE=en_US.UTF-8
 [5] LC_MONETARY=en_US.UTF-8    LC_MESSAGES=en_US.UTF-8
 [7] LC_PAPER=en_US.UTF-8       LC_NAME=C
 [9] LC_ADDRESS=C               LC_TELEPHONE=C
[11] LC_MEASUREMENT=en_US.UTF-8 LC_IDENTIFICATION=C

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

other attached packages:
[1] shiny_0.12.1 Rcpp_0.11.6

loaded via a namespace (and not attached):
[1] R6_2.0.1        htmltools_0.2.6 digest_0.6.8    xtable_1.7-4
[5] httpuv_1.3.2    mime_0.3

Thanks in advance for any pointers or help.

Answer 1

Apparently, it was a library/permissions issue. I am still a bit foggy on R package managment and all the possible different library locations (certainly when working with Rstudio server and shiny server and bioconductor etc.) and when or not to use sudo to install packages. Any good guidelines on that would probably have avoided this question.

The code suggested by the people at Rstudio ( sudo su -\\ -c "R -e \\"install.packages('shiny', repos='http://cran.rstudio.com/')\\"" ) got me thinking: when I run just R in the terminal or sudo R the library(Rcpp) and library(shiny) work so I just did sudo su and then ran R interactively with install.packages('shiny', repos='http://cran.rstudio.com/') . This showed that apparently for the root user (su) the Rcpp package was not installed (!). After manually installing the package I could also re-install shiny and my shiny app started working again.

What concerns me still about this is how the Rcpp package "dissappeared" in the first place from the root R packages. I cannot remember removing it myself and would find it rather unpleasant behavior if an update would have caused this.

Either way: the issue is resolved. Maybe this answer can help others with a similar issue.