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@r-project.org>, Jeffrey Horner <
jeff.horner@vanderbilt.edu>
Maintainer: Simon Urbanek <Simon.Urbanek@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

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