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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