[R] Cairo package error: "unable to load..."

[Simon Urbanek]

Leonardo,

you don't have X11 installed and it no longer ships with OS X 10.9 - you need to get it from

http://xquartz.macosforge.org

Cheers,
Simon


On Jul 23, 2014, at 9:25 PM, Leonardo Gama <leonardo.gama at usp.br> wrote:

> Hi!
> 
> I've just installed R on my OS X 10.9 and was trying to make arrayQualityMetrics package work. I've installed it via the biocLite Bioconductor script, and everything was apparently fine. But when I tried to load the package, I've got an issue with the Cairo package...
> 
> Then I tried to load only Cairo:
> 
> > library("Cairo")
> 
> Error : .onLoad failed in loadNamespace() for 'Cairo', details:
>   call: dyn.load(file, DLLpath = DLLpath, ...)
>   error: unable to load shared object '/Library/Frameworks/R.framework/Versions/3.1/Resources/library/Cairo/libs/Cairo.so':
>   dlopen(/Library/Frameworks/R.framework/Versions/3.1/Resources/library/Cairo/libs/Cairo.so, 6): Library not loaded: /opt/X11/lib/libXrender.1.dylib
>   Referenced from: /Library/Frameworks/R.framework/Versions/3.1/Resources/library/Cairo/libs/Cairo.so
>   Reason: image not found
> Error: package or namespace load failed for ‘Cairo’
> 
> > traceback()
> 
> 2: stop(gettextf("package or namespace load failed for %s", sQuote(package)), 
>        call. = FALSE, domain = NA)
> 1: library(Cairo)
> 
> 
> Verified it version and dependencies:
> 
> > packageDescription("Cairo")
> 
> Package: Cairo
> Version: 1.5-6
> Title: [...]
> Author: Simon Urbanek <Simon.Urbanek at r-project.org>, Jeffrey Horner <jeff.horner at vanderbilt.edu>
> Maintainer: Simon Urbanek <Simon.Urbanek at r-project.org>
> Depends: R (>= 2.4.0)
> Suggests: png
> Enhances: FastRWeb
> Description: [...]
> SystemRequirements: cairo (>= 1.2 http://www.cairographics.org/)
> URL: http://www.rforge.net/Cairo/
> Packaged: 2014-06-26 14:50:25 UTC; svnuser
> NeedsCompilation: yes
> Repository: CRAN
> Date/Publication: 2014-06-26 17:15:22
> Built: R 3.1.0; x86_64-apple-darwin13.1.0; 2014-06-27 05:04:27 UTC;
>         unix
> -- File: /Library/Frameworks/R.framework/Versions/3.1/Resources/library/Cairo/Meta/package.rds
> 
> 
> Tried to update it and got another error/warning:
> 
> > upgrade.packages("Cairo")
> 
> Warning message:
> In doTryCatch(return(expr), name, parentenv, handler) :
>   unable to load shared object '/Library/Frameworks/R.framework/Resources/modules//R_X11.so':
>   dlopen(/Library/Frameworks/R.framework/Resources/modules//R_X11.so, 6): Library not loaded: /opt/X11/lib/libSM.6.dylib
>   Referenced from: /Library/Frameworks/R.framework/Resources/modules//R_X11.so
>   Reason: image not found
> 
> > traceback()
> 
> No traceback available
> 
>  
> And finally:
> 
> > sessionInfo()
> 
> R version 3.1.1 (2014-07-10)
> Platform: x86_64-apple-darwin13.1.0 (64-bit)
> 
> locale:
> [1] C/UTF-8/C/C/C/C
> 
> attached base packages:
> [1] stats     graphics  grDevices utils     datasets  methods   base     
> 
> loaded via a namespace (and not attached):
> [1] tools_3.1.1
> > pack
> packBits               packageEvent           packageSlot            packageStatus
> package.skeleton       packageHasNamespace    packageSlot<-          packageVersion
> packageDescription     packageName            packageStartupMessage  package_version
> 
> 
> I've also verified the cairo.os file cited in the first error message, and it was there:
> 
> $ file /Library/Frameworks/R.framework/Versions/3.1/Resources/library/Cairo/libs/Cairo.so
> 
> /Library/Frameworks/R.framework/Versions/3.1/Resources/library/Cairo/libs/Cairo.so: Mach-O 64-bit dynamically linked shared library x86_64
> 
> $ ls -lh /Library/Frameworks/R.framework/Versions/3.1/Resources/library/Cairo/libs/Cairo.so
> 
> -rwxrwxr-x  1 root  admin   3.2M Jun 27 02:04 /Library/Frameworks/R.framework/Versions/3.1/Resources/library/Cairo/libs/Cairo.so
> 
> 
> I have no idea of what's going wrong. Somebody could help me?
> Thank you, and sorry for the bad English.
> 
> -- 
> Leonardo Gama, acadêmico
> Ciências Moleculares / Medicina
> Universidade de São Paulo, Brasil