On Jul 24, 2014, at 12:03 PM, Leonardo Gama <leonardo.g...@usp.br> wrote:
> Sorry, Simon. I should have suspected that it was a trivial problem. But > there was an X11 app icon in Applications and I assumed it was installed, but > was not. This mensgem only appeared when I clicked on such icon: > > <Screen Shot 2014-07-24 at 11.44.31 AM.png> > Yes, as you can see it says "X11 is *no longer* included with OS X" [...] and it asks you if you want to know how to install it - if you continue, it will point you to a page that says that you have to download it from http://xquartz.macosforge.org It doesn't actually do anything - you have to install it yourself - it just tells you how. Cheers, Simon > Thank you again! > > Leonardo > > > 2014-07-24 10:43 GMT-03:00 Simon Urbanek <simon.urba...@r-project.org>: > 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.g...@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.urba...@r-project.org>, Jeffrey Horner > > <jeff.hor...@vanderbilt.edu> > > Maintainer: Simon Urbanek <simon.urba...@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 > > > > > -- > Leonardo Gama, acadêmico > Ciências Moleculares / Medicina > Universidade de São Paulo, Brasil ______________________________________________ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
