Re: [R-SIG-Mac] Cannot list Bioconductor packages
On 23 Apr 2015, at 12:53, peter dalgaard pda...@gmail.com wrote: Looks like R.app forgot to adapt to tools:::.BioC_version_associated_with_R_version function () numeric_version(Sys.getenv(R_BIOC_VERSION, 3.1)) bytecode: 0x7fd10ac08d50 environment: namespace:tools I.e. in newer R, you need to use tools:::.BioC_version_associated_with_R_version() to get the version. You might want to check newer R.app builds off of http://r.research.att.com or wait for Simon to chime in with harder info than what I have. Just tried R.app GUI 1.66 (6935) x86_64-apple-darwin13.4.0 and I have the same message: Error in as.character(tools:::.BioC_version_associated_with_R_version) : cannot coerce type 'closure' to vector of type 'character' Or,... You could just edit the offending R file by hand. If neither of us have done anything out of the ordinary, I think you'll find it in /Applications/R.app/Contents/Resources/GUI-tools.R Hence I edited GUI-tool.R by hand — which works. BW F Or,... Upon actually reading the above code section, I think that a noninvasive procedure is preemptively to use options(BioC.repos= z) where z is obtained from, um, mirror - getOption(BioC_mirror, http://www.bioconductor.org;) # ver - 3.1 ver - as.character(tools:::.BioC_version_associated_with_R_version()) z - paste(mirror, packages, ver, c(bioc, data/annotation, data/experiment, extra), sep = /)) -Peter D. On 23 Apr 2015, at 09:58 , Federico Calboli federico.calb...@helsinki.fi wrote: Hi All, I am using R version 3.2.0 (2015-04-16) and R.app GUI 1.65 (6931) x86_64-apple-darwin13.4.0. I am using the package installer to install and update packages. I have the following problem: when I try and list Bioconductor packages (binaries or source) I get the following message: Error in as.character(tools:::.BioC_version_associated_with_R_version) : cannot coerce type 'closure' to vector of type 'character' No idea what is going on or how to fix it, and in fact I have no idea whetehr this is a OS X specific issue or not (but I cannot test on a different OS). If this *is* a OS X issue I would be grateful if someone can figure out what’s missing. Best F -- Federico Calboli Ecological Genetics Research Unit Department of Biosciences PO Box 65 (Biocenter 3, Viikinkaari 1) FIN-00014 University of Helsinki Finland federico.calb...@helsinki.fi ___ R-SIG-Mac mailing list R-SIG-Mac@r-project.org https://stat.ethz.ch/mailman/listinfo/r-sig-mac -- Peter Dalgaard, Professor, Center for Statistics, Copenhagen Business School Solbjerg Plads 3, 2000 Frederiksberg, Denmark Phone: (+45)38153501 Office: A 4.23 Email: pd@cbs.dk Priv: pda...@gmail.com -- Federico Calboli Ecological Genetics Research Unit Department of Biosciences PO Box 65 (Biocenter 3, Viikinkaari 1) FIN-00014 University of Helsinki Finland federico.calb...@helsinki.fi ___ R-SIG-Mac mailing list R-SIG-Mac@r-project.org https://stat.ethz.ch/mailman/listinfo/r-sig-mac
Re: [R-SIG-Mac] cairo devices not working in 3.2.0
Apologies, I meant `cairo_ps()` yields an error, rather than `cairo_png()`, and Yosemite rather than Mavericks. My session info: sessionInfo() R version 3.2.0 (2015-04-16) Platform: x86_64-apple-darwin13.4.0 (64-bit) Running under: OS X 10.10.2 (Yosemite) locale: [1] en_US.UTF-8/en_US.UTF-8/en_US.UTF-8/C/en_US.UTF-8/en_US.UTF-8 attached base packages: [1] stats graphics grDevices utils datasets methods base loaded via a namespace (and not attached): [1] tools_3.2.0 On Fri, Apr 24, 2015 at 7:39 AM Brandon Hurr bhiv...@gmail.com wrote: Noam, I've just recently upgraded too and everything works except cairo_png(). capabilities(cairo) cairo TRUE svg() cairo_png() Error: could not find function cairo_png cairo_pdf() sessionInfo() R version 3.2.0 (2015-04-16) Platform: x86_64-apple-darwin13.4.0 (64-bit) Running under: OS X 10.10.3 (Yosemite) locale: [1] en_US.UTF-8/en_US.UTF-8/en_US.UTF-8/C/en_US.UTF-8/en_US.UTF-8 attached base packages: [1] stats graphics grDevices utils datasets methods base Brandon [[alternative HTML version deleted]] ___ R-SIG-Mac mailing list R-SIG-Mac@r-project.org https://stat.ethz.ch/mailman/listinfo/r-sig-mac
Re: [R-SIG-Mac] cairo devices not working in 3.2.0
Noam, I've just recently upgraded too and everything works except cairo_png(). capabilities(cairo) cairo TRUE svg() cairo_png() Error: could not find function cairo_png cairo_pdf() sessionInfo() R version 3.2.0 (2015-04-16) Platform: x86_64-apple-darwin13.4.0 (64-bit) Running under: OS X 10.10.3 (Yosemite) locale: [1] en_US.UTF-8/en_US.UTF-8/en_US.UTF-8/C/en_US.UTF-8/en_US.UTF-8 attached base packages: [1] stats graphics grDevices utils datasets methods base Brandon ___ R-SIG-Mac mailing list R-SIG-Mac@r-project.org https://stat.ethz.ch/mailman/listinfo/r-sig-mac
Re: [R-SIG-Mac] cairo devices not working in 3.2.0
I had this issue but it went away when I installed the 3.2-patched binary. On Apr 24, 2015, at 10:52 AM, Noam Ross noam.r...@gmail.com wrote: Apologies, I meant `cairo_ps()` yields an error, rather than `cairo_png()`, and Yosemite rather than Mavericks. My session info: sessionInfo() R version 3.2.0 (2015-04-16) Platform: x86_64-apple-darwin13.4.0 (64-bit) Running under: OS X 10.10.2 (Yosemite) locale: [1] en_US.UTF-8/en_US.UTF-8/en_US.UTF-8/C/en_US.UTF-8/en_US.UTF-8 attached base packages: [1] stats graphics grDevices utils datasets methods base loaded via a namespace (and not attached): [1] tools_3.2.0 On Fri, Apr 24, 2015 at 7:39 AM Brandon Hurr bhiv...@gmail.com wrote: Noam, I've just recently upgraded too and everything works except cairo_png(). capabilities(cairo) cairo TRUE svg() cairo_png() Error: could not find function cairo_png cairo_pdf() sessionInfo() R version 3.2.0 (2015-04-16) Platform: x86_64-apple-darwin13.4.0 (64-bit) Running under: OS X 10.10.3 (Yosemite) locale: [1] en_US.UTF-8/en_US.UTF-8/en_US.UTF-8/C/en_US.UTF-8/en_US.UTF-8 attached base packages: [1] stats graphics grDevices utils datasets methods base Brandon [[alternative HTML version deleted]] ___ R-SIG-Mac mailing list R-SIG-Mac@r-project.org https://stat.ethz.ch/mailman/listinfo/r-sig-mac ___ R-SIG-Mac mailing list R-SIG-Mac@r-project.org https://stat.ethz.ch/mailman/listinfo/r-sig-mac
[R-SIG-Mac] cairo devices not working in 3.2.0
I recently upgraded to 3.2.0 on OSX Mavericks, and found that cairo devices do not work. capabilities(cairo) cairo FALSE If I run `svg()`, `cairo_png()` or `cairo_pdf()`, I get an error similar to this: In cairo_pdf(tf, width, height, pointsize, FALSE, family, bg, antialias) : unable to load shared object '/Library/Frameworks/R.framework/Resources/library/grDevices/libs//cairo.so': dlopen(/Library/Frameworks/R.framework/Resources/library/grDevices/libs//cairo.so, 6): image not found If revert to 3.1.3 by re-installing the binary, `capabilities(cairo)` is TRUE, and these devices work fine. Is this a bug or expected behavior? [[alternative HTML version deleted]] ___ R-SIG-Mac mailing list R-SIG-Mac@r-project.org https://stat.ethz.ch/mailman/listinfo/r-sig-mac
Re: [R-SIG-Mac] cairo devices not working in 3.2.0
My cairo problems went away after reinstalling xQuartz + R 3.2.0 and rebooting. On Fri, Apr 24, 2015 at 8:05 AM, Amos B. Elberg amos.elb...@gmail.com wrote: I had this issue but it went away when I installed the 3.2-patched binary. On Apr 24, 2015, at 10:52 AM, Noam Ross noam.r...@gmail.com wrote: Apologies, I meant `cairo_ps()` yields an error, rather than `cairo_png()`, and Yosemite rather than Mavericks. My session info: sessionInfo() R version 3.2.0 (2015-04-16) Platform: x86_64-apple-darwin13.4.0 (64-bit) Running under: OS X 10.10.2 (Yosemite) locale: [1] en_US.UTF-8/en_US.UTF-8/en_US.UTF-8/C/en_US.UTF-8/en_US.UTF-8 attached base packages: [1] stats graphics grDevices utils datasets methods base loaded via a namespace (and not attached): [1] tools_3.2.0 On Fri, Apr 24, 2015 at 7:39 AM Brandon Hurr bhiv...@gmail.com wrote: Noam, I've just recently upgraded too and everything works except cairo_png(). capabilities(cairo) cairo TRUE svg() cairo_png() Error: could not find function cairo_png cairo_pdf() sessionInfo() R version 3.2.0 (2015-04-16) Platform: x86_64-apple-darwin13.4.0 (64-bit) Running under: OS X 10.10.3 (Yosemite) locale: [1] en_US.UTF-8/en_US.UTF-8/en_US.UTF-8/C/en_US.UTF-8/en_US.UTF-8 attached base packages: [1] stats graphics grDevices utils datasets methods base Brandon [[alternative HTML version deleted]] ___ R-SIG-Mac mailing list R-SIG-Mac@r-project.org https://stat.ethz.ch/mailman/listinfo/r-sig-mac ___ R-SIG-Mac mailing list R-SIG-Mac@r-project.org https://stat.ethz.ch/mailman/listinfo/r-sig-mac ___ R-SIG-Mac mailing list R-SIG-Mac@r-project.org https://stat.ethz.ch/mailman/listinfo/r-sig-mac
