Error: .onLoad failed in loadNamespace()

[Patrick Toche]

Dear all,

I have a shiny app that allows the user to upload a dataset and make some ggplots. It works fine locally, but produces the following error message on the rstudio server:

Error: .onLoad failed in loadNamespace() for 'Cairo', details: call: dyn.load(file, DLLpath = DLLpath, ...) error: unable to load shared object '/home/toche/R/library/Cairo/libs/Cairo.so': libxcb-shm.so.0: failed to map segment from shared object: Cannot allocate memory

I load the following packages:

library("shiny")

library("gdata")

installXLSXsupport() # support for xlsx format

library("XLConnect") # support for xlsx format

library("reshape2")# provides function melt

library("plyr")

library("ggplot2")

library("grid") # provides function unit() for ggplot2

library("scales") # provides scale_x_y() and pretty_breaks() for ggplot2

I did install and update all the packages, by running: 

install.packages("shiny", dependencies = TRUE)

on all of them except "grid" which appears to be included in R now (?)

I also did:

install.packages("cairoDevice", dependencies = TRUE)

install.packages("Cairo.so", dependencies = TRUE)

install.packages("rJava", dependencies = TRUE)

I also read this exchange:

https://groups.google.com/forum/#!msg/shiny-discuss/aPaAPQpVkdM/pnqgfrTjSNYJ

so I commented out: library("XLConnect") and installXLSXsupport() 

but the error persists.

Any suggestions?

Thanks!

[Winston Chang]

Have you tried:

install.packages('Cairo')

library(Cairo)

-Winston

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[Patrick Toche]

Have you tried:

install.packages('Cairo')

library(Cairo)

Thanks for your help Winston. 

I hadn't loaded the package before with library("Cairo"), assuming that since I had no need to load it locally I didn't need to load it on the server.

Now, after loading the "Cairo" library, the error message is:

The application unexpectedly exited.

Diagnostic information has been dumped to the JavaScript error console.

Here is what happens. 1. The application freezes for some time. 2. When it appears to be loaded, the conditionalPanel is open (as opposed to closed) and the area where the plots are supposed to be is black instead of the usual white. 3. When I load a dataset, the app crashes with a "memory" error message that is too quick for me to read properly. After that it hangs (dark grey colour, unresponsive).

However, I seem to have narrowed down the problem to the installXLSXsupport() function of the gdata package. I think.

I commented out as follows:

#library("gdata")

#installXLSXsupport() # support for xlsx format with gdata package

after that the app loads and works properly for a csv file. The plot area is black, rather than white, before a plot is produced, which is something I'd like to fix too. 

However, if I load an xlsx file (silly I know), I get in various places:

Error: could not find function "loadWorkbook"

Error: could not find function "getSheets"

I'm going to investigate that as soon as I can.

Thanks Winston.

[Patrick Toche]

However, I seem to have narrowed down the problem to the installXLSXsupport() function of the gdata package. I think.

I spoke too fast. The problem is rather with package "XLConnect". 

Here a slightly edited copy of the console output after installing the package. Perhaps you can help me "read" the error messages and take action. Thanks!

Some problem with dependency package RcppArmadillo it seems?

> install.packages("XLConnect", dependencies = TRUE)

Installing package(s) into ‘/home/toche/R/library’

(as ‘lib’ is unspecified)

--- Please select a CRAN mirror for use in this session ---

DELETED LIST OF MIRRORS HERE

Warning: dependency ‘Rcpp’ is not available

also installing the dependencies ‘RcppArmadillo’, ‘forecast’

trying URL 'http://cran.wustl.edu/src/contrib/RcppArmadillo_0.3.920.3.tar.gz'

Content type 'application/x-gzip' length 866795 bytes (846 Kb)

opened URL

==================================================

downloaded 846 Kb

trying URL 'http://cran.wustl.edu/src/contrib/forecast_4.8.tar.gz'

Content type 'application/x-gzip' length 142778 bytes (139 Kb)

opened URL

==================================================

downloaded 139 Kb

trying URL 'http://cran.wustl.edu/src/contrib/XLConnect_0.2-5.tar.gz'

Content type 'application/x-gzip' length 18223083 bytes (17.4 Mb)

opened URL

==================================================

downloaded 17.4 Mb

* installing *source* package ‘RcppArmadillo’ ...

** package ‘RcppArmadillo’ successfully unpacked and MD5 sums checked

** libs

g++ -I/usr/share/R/include -DNDEBUG   -I"/usr/local/lib/R/site-library/Rcpp/include"  -I../inst/include -fpic  -O3 -pipe  -g  -c RcppArmadillo.cpp -o RcppArmadillo.o

In file included from ../inst/include/RcppArmadillo.h:30:0,

                 from RcppArmadillo.cpp:22:

../inst/include/RcppArmadilloForward.h:99:33: error: ‘ConstReferenceInputParameter’ is not a template

../inst/include/RcppArmadilloForward.h:100:33: error: ‘ReferenceInputParameter’ is not a template

../inst/include/RcppArmadilloForward.h:101:33: error: ‘ConstInputParameter’ is not a template

make: *** [RcppArmadillo.o] Error 1

ERROR: compilation failed for package ‘RcppArmadillo’

* removing ‘/home/toche/R/library/RcppArmadillo’

* installing *source* package ‘XLConnect’ ...

** package ‘XLConnect’ successfully unpacked and MD5 sums checked

** R

** demo

** inst

** preparing package for lazy loading

Creating a generic function for ‘print’ from package ‘base’ in package ‘XLConnect’

Creating a generic function for ‘summary’ from package ‘base’ in package ‘XLConnect’

** help

*** installing help indices

** building package indices

** installing vignettes

   ‘XLConnect.Rnw’ using ‘latin1’ 

   ‘XLConnectImpatient.Rnw’ using ‘latin1’ 

** testing if installed package can be loaded

* DONE (XLConnect)

ERROR: dependency ‘RcppArmadillo’ is not available for package ‘forecast’

* removing ‘/home/toche/R/library/forecast’

The downloaded source packages are in

‘/tmp/RtmpyYpBUY/downloaded_packages’

Warning messages:

1: In install.packages("XLConnect", dependencies = TRUE) :

  installation of package ‘RcppArmadillo’ had non-zero exit status

2: In install.packages("XLConnect", dependencies = TRUE) :

  installation of package ‘forecast’ had non-zero exit status

>  

[Patrick Toche]

How about this?

install.packages("RcppArmadillo")

Installing package(s) into ‘/home/toche/R/library’

(as ‘lib’ is unspecified)

Error: memory exhausted (limit reached?)

[Patrick Toche]

could I be running out of memory?

I only have 4 very simple apps. Below is a list of packages, mostly dependencies. Any of those unnecessary and/or taking up unreasonable space? Big libraries are always listed as having 4.0K...

I deleted a few libraries that I know I'm not using and tried again. Here is the console output: It looks like a problem with RcppArmadillo, no? I tried several different repositories, just in case.

installing *source* package ‘RcppArmadillo’ ...

** package ‘RcppArmadillo’ successfully unpacked and MD5 sums checked

** libs

g++ -I/usr/share/R/include -DNDEBUG   -I"/usr/local/lib/R/site-library/Rcpp/include"  -I../inst/include -fpic  -O3 -pipe  -g  -c RcppArmadillo.cpp -o RcppArmadillo.o

In file included from ../inst/include/RcppArmadillo.h:30:0,

                 from RcppArmadillo.cpp:22:

../inst/include/RcppArmadilloForward.h:99:33: error: ‘ConstReferenceInputParameter’ is not a template

../inst/include/RcppArmadilloForward.h:100:33: error: ‘ReferenceInputParameter’ is not a template

../inst/include/RcppArmadilloForward.h:101:33: error: ‘ConstInputParameter’ is not a template

make: *** [RcppArmadillo.o] Error 1

ERROR: compilation failed for package ‘RcppArmadillo’

* removing ‘/home/toche/R/library/RcppArmadillo’

The downloaded source packages are in

‘/tmp/Rtmpy79MpU/downloaded_packages’

Warning message:

In install.packages("RcppArmadillo", dependencies = TRUE) :

  installation of package ‘RcppArmadillo’ had non-zero exit status

toche@spark:~/R/library$ ls -lah

total 88K

drwxrwxr-x 73 toche toche 4.0K Dec  4 05:40 .

drwxrwxr-x  3 toche toche   20 Nov 11 14:06 ..

drwxr-xr-x  6 toche toche   93 Dec  3 22:28 abind

drwxr-xr-x  7 toche toche  104 Dec  3 21:20 bitops

drwxr-xr-x  6 toche toche 4.0K Nov 11 14:09 brew

drwxr-xr-x  7 toche toche  115 Dec  3 22:53 Cairo

drwxr-xr-x  7 toche toche  104 Dec  3 22:39 caTools

drwxr-xr-x  9 toche toche  139 Dec  3 21:21 cluster

drwxr-xr-x  6 toche toche   93 Dec  3 21:21 codetools

drwxr-xr-x  9 toche toche 4.0K Nov 11 14:12 colorspace

drwxr-xr-x  8 toche toche  120 Dec  3 22:33 devtools

drwxr-xr-x  7 toche toche  104 Nov 11 14:12 dichromat

drwxr-xr-x  7 toche toche  116 Dec  3 21:20 digest

drwxr-xr-x 10 toche toche  156 Dec  3 22:29 doMC

drwxr-xr-x  7 toche toche  116 Nov 11 14:07 evaluate

drwxr-xr-x  8 toche toche  149 Dec  3 22:31 fImport

drwxr-xr-x 10 toche toche  156 Dec  3 22:29 foreach

drwxr-xr-x  8 toche toche  127 Nov 11 14:09 formatR

drwxr-xr-x  7 toche toche  129 Nov 11 14:13 Formula

drwxr-xr-x  7 toche toche  104 Dec  3 22:30 fracdiff

drwxr-xr-x 12 toche toche 4.0K Dec  3 22:55 gdata

drwxr-xr-x 10 toche toche 4.0K Dec  3 22:54 ggplot2

drwxr-xr-x  7 toche toche  116 Nov 11 14:13 gtable

drwxr-xr-x  8 toche toche  142 Dec  3 21:44 gtools

drwxr-xr-x  9 toche toche  125 Nov 11 14:13 hexbin

drwxr-xr-x  7 toche toche  114 Nov 11 14:09 highr

drwxr-xr-x  7 toche toche 4.0K Dec  3 21:19 Hmisc

drwxr-xr-x  8 toche toche  140 Nov 11 14:07 httpuv

drwxr-xr-x  8 toche toche  127 Nov 11 14:09 httr

drwxr-xr-x  9 toche toche  134 Dec  3 22:28 iterators

drwxr-xr-x  7 toche toche  119 Dec  3 22:29 itertools

drwxr-xr-x 14 toche toche 4.0K Nov 11 14:09 knitr

drwxr-xr-x  6 toche toche   93 Nov 11 14:13 labeling

drwxr-xr-x 10 toche toche 4.0K Dec  3 21:21 lattice

drwxr-xr-x  7 toche toche  118 Nov 11 14:14 mapproj

drwxr-xr-x  9 toche toche  129 Nov 11 14:13 maps

drwxr-xr-x 12 toche toche 4.0K Nov 11 14:14 maptools

drwxr-xr-x 11 toche toche 4.0K Nov 11 14:07 markdown

drwxr-xr-x 12 toche toche 4.0K Dec  3 21:24 Matrix

drwxr-xr-x  6 toche toche   93 Nov 11 14:09 memoise

drwxr-xr-x  8 toche toche  130 Dec  3 21:25 mgcv

drwxr-xr-x 11 toche toche 4.0K Nov 11 14:14 multcomp

drwxr-xr-x  7 toche toche  128 Nov 11 14:13 munsell

drwxr-xr-x  8 toche toche  140 Nov 11 14:13 mvtnorm

drwxr-xr-x  8 toche toche  139 Dec  3 21:21 nnet

drwxr-xr-x  9 toche toche  153 Dec  3 22:56 plyr

drwxr-xr-x  8 toche toche  125 Dec  3 22:31 png

drwxr-xr-x  8 toche toche 4.0K Nov 11 14:13 proto

drwxr-xr-x  7 toche toche  104 Dec  3 22:30 quadprog

drwxr-xr-x 10 toche toche 4.0K Nov 11 14:13 quantreg

drwxr-xr-x  6 toche toche  107 Nov 11 14:12 RColorBrewer

drwxr-xr-x 13 toche toche 4.0K Dec  3 22:34 RCurl

drwxr-xr-x  8 toche toche  142 Dec  3 22:56 reshape2

drwxr-xr-x  8 toche toche  126 Nov 11 14:09 roxygen2

drwxr-xr-x 10 toche toche  148 Dec  3 21:21 rpart

drwxr-xr-x 10 toche toche 4.0K Dec  3 22:30 RUnit

drwxr-xr-x  8 toche toche  140 Nov 11 14:13 sandwich

drwxr-xr-x  7 toche toche  116 Dec  3 22:57 scales

drwxr-xr-x 10 toche toche 4.0K Dec  3 22:29 shiny

drwxr-xr-x  9 toche toche  151 Nov 11 14:12 shinyIncubator

drwxr-xr-x 12 toche toche 4.0K Nov 11 14:13 sp

drwxr-xr-x 11 toche toche 4.0K Nov 11 14:13 SparseM

drwxr-xr-x  7 toche toche  116 Nov 11 14:06 stringr

drwxr-xr-x  9 toche toche  154 Dec  3 21:21 survival

drwxr-xr-x  7 toche toche  116 Nov 11 14:07 testthat

drwxr-xr-x  7 toche toche  106 Nov 11 14:13 TH.data

drwxr-xr-x  7 toche toche  130 Dec  3 22:30 timeDate

drwxr-xr-x  8 toche toche 4.0K Dec  3 22:31 timeSeries

drwxr-xr-x  8 toche toche  130 Dec  3 22:31 tseries

drwxr-xr-x  8 toche toche  128 Nov 11 14:09 whisker

drwxr-xr-x 11 toche toche 4.0K Dec  4 05:40 XLConnect

drwxr-xr-x 10 toche toche  151 Dec  3 22:34 XML

drwxr-xr-x  9 toche toche  151 Nov 11 14:12 zoo

toche@spark:~/R/library$ 

[Patrick Toche]

I copied the whole RcppArmadillo directory from my laptop to the remote library directory:

$ scp -r /tmp/RcppArmadillo to...@spark.rstudio.com:R/library/

Not helping however...

RcppArmadillo is in the library directory now:

toche@spark:~/R/library$ ls

abind       evaluate  Hmisc      memoise       RcppArmadillo   stringr

bitops      fImport   httpuv     mgcv          RCurl           survival

brew        foreach   httr       multcomp      reshape2        testthat

Cairo       formatR   iterators  munsell       roxygen2        TH.data

caTools     Formula   itertools  mvtnorm       rpart           timeDate

cluster     fracdiff  labeling   nnet          RUnit           timeSeries

codetools   gdata     lattice    plyr          sandwich        tseries

colorspace  ggplot2   mapproj    png           scales          whisker

devtools    gtable    maps       proto         shiny           XLConnect

dichromat   gtools    maptools   quadprog      shinyIncubator  XML

digest      hexbin    markdown   quantreg      sp              zoo

doMC        highr     Matrix     RColorBrewer  SparseM

toche@spark:~/R/library$ 

[Patrick Toche]

Just wondering about this: when I log in to spark.rstudio.com, it tells me that:

1) memory usage is 52% (or maybe 9.9%) so there should be no memory problem

2) there are 2 zombie processes: doesn't sound good. Should I do something about these zombies?

3) there's a whole bunch of packages that need updating. Is there a command I have to run to update these?

Sorry, total newbie. Thanks!

ssh to...@spark.rstudio.com

to...@spark.rstudio.com's password: 

Welcome to Ubuntu 12.04.2 LTS (GNU/Linux 3.2.0-45-virtual x86_64)

 * Documentation:  https://help.ubuntu.com/

  System information as of Wed Dec  4 06:30:18 UTC 2013

  System load:    3.72                Processes:           414

  Usage of /home: 9.9% of 1023.50GB   Users logged in:     2

  Memory usage:   52%                 IP address for eth0: 10.253.29.69

  Swap usage:     0%

  => There are 2 zombie processes.

  Graph this data and manage this system at https://landscape.canonical.com/

214 packages can be updated.

116 updates are security updates.

[Winston Chang]

Hi Patrick -

I think you may be running into issues related to the slightly older version of R (2.15.2) that we have installed on Glimmer and Spark. Unfortunately, upgrading R on those servers has the potential to break everyone's Shiny apps.

We've been putting our efforts into setting up a new hosting service, which will let you use the latest version of R. You can sign up for the alpha here, and we'll get you set up right away: http://shinyapps.io

-Winston

[Patrick Toche]

Thanks Winston, just did!

[Patrick Toche]

It looks like the problem persists. Something related to rJava. Any suggestions? Thanks!

> deployApp()

Preparing to deploy application...DONE

Uploading application bundle...DONE

Deploying application...

Waiting for task: 15219

  building: Building 25 packages

  building: Building package xtable-1.7-1

  building: Building package labeling-0.2

  building: Building package Cairo-1.5-2

Error: Unhandled Exception: Child Task 15220 error: Unhandled Exception: Child Task 15223 failed: Error building package: Error building Cairo (1.5-2). Image build exited with non-zero status: 1

> deployApp()

...

Deploying application...

Waiting for task: 15224

  building: Building 22 packages

  building: Building package stringr-0.6.2

  building: Building package plyr-1.8

  building: Building package RColorBrewer-1.0-5

  building: Building package proto-0.3-10

  building: Building package dichromat-2.0-0

  building: Building package bitops-1.0-6

  building: Building package caTools-1.16

  building: Building package digest-0.6.3

  building: Building package gtable-0.1.2

  building: Building package lattice-0.20-24

  building: Building package reshape2-1.2.2

  building: Building package MASS-7.3-29

  building: Building package colorspace-1.2-4

  building: Building package munsell-0.4.2

  building: Building package scales-0.2.3

  building: Building package RJSONIO-1.0-3

  building: Building package ggplot2-0.9.3.1

  building: Building package Rcpp-0.10.5

  building: Building package httpuv-1.2.0

  building: Building package rJava-0.9-4

Error: Unhandled Exception: Child Task 15225 error: Unhandled Exception: Child Task 15245 failed: Error building package: Error building rJava (0.9-4). Image build exited with non-zero status: 1

[Winston Chang]

Hi Andy -

One of our ShinyApps users is having trouble with rJava. We've encountered this on glimmer and spark in the past. The workaround was to run the following:

    _JAVA_OPTIONS=-Xmx256m R CMD javareconf

... although I believe we had a configuration change along the way which prevents this from working now. The r::rjava recipe in the deploy-test repo has comments with a little more information about it.

-Winston

[Winston Chang]

Hi Patrick - I forwarded your message to Andy Kipp <an...@rstudio.com>, who will be able to look into the issue with ShinyApps. (I also accidentally sent an extra copy of the message to this list.)

-Winston

[Patrick Toche]

Thanks Winston!

Below is the version of rJava I have on my laptop, where I'm not experiencing any problems.

Package: rJava

Version: 0.9-4

Title: Low-level R to Java interface

Author: Simon Urbanek <simon....@r-project.org>

Maintainer: Simon Urbanek <simon....@r-project.org>

Depends: R (>= 2.5.0), methods

Description: Low-level interface to Java VM very much like .C/.Call and

        friends. Allows creation of objects, calling methods and

        accessing fields.

License: GPL-2

URL: http://www.rforge.net/rJava/

SystemRequirements: java

Packaged: 2013-03-11 16:02:23 UTC; svnuser

NeedsCompilation: yes

Repository: CRAN

Date/Publication: 2013-03-12 10:54:30

Built: R 3.0.0; x86_64-apple-darwin10.8.0; 2013-04-03 15:15:11 UTC; unix

Archs: rJava.so.dSYM

[Patrick Toche]

I copied the rJava folder I have in my R library in my laptop to the server, but here's the message I get now when I try to load the app:

Loading required package: rJava Warning: package ‘rJava’ was built under R version 3.0.0 Error: package ‘rJava’ was built for x86_64-apple-darwin10.8.0 Execution halted




I don't get this message on my laptop.

[Patrick Toche]

The bottom line is that rJava is not currently supported, so that pretty much rules out using the Java-based "XLConnect" library I was using to load and read xlsx files. One workaround is to use the Perl-based "gdata" library. 

I had to alter the code a little, to replace functions provided by the XLConnect library. For instance:

#      , 'choices' = getSheets(loadWorkbook(input$dataset$datapath))# package "XLConnect"

      , 'choices' = sheetNames(input$dataset$datapath)# package "gdata"

Another approach is to use the xlsxToR function written by Schaun Wheeler or the version modified by Zheng that is supposed to be more efficient. References:

https://gist.github.com/schaunwheeler/5825002

http://www.milanor.net/blog/?p=779

Thanks to all for your feedback. My app now runs smoothly on the server.  :-)

[Shreeram Iyer]

Error in library.dynam(lib, package, package.lib) : shared object ‘digest.so’ not found Error: package or namespace load failed for ‘shiny’ Execution halted