[R-SIG-Mac] mac mavericks problem
one of my students just download mac mavericks. starting with the new system, R-3.0.1 in the APP is misbehaving. enter TRUE - FALSE (to illustrate why use of T is not a good practice) R app gives the error message invalid (do_set) left-hand side to assignment *** caught segfault *** address 0x7c0, cause 'memory not mapped' Possible actions 1 2 3 4 The R program run in the terminal behaves correctly. it reports the invalid assignment and then gives a normal R prompt. Will this happen in R-3.0.2? (yes we will download and check that). ___ R-SIG-Mac mailing list R-SIG-Mac@r-project.org https://stat.ethz.ch/mailman/listinfo/r-sig-mac
Re: [R-SIG-Mac] mac mavericks problem
On Oct 24, 2013, at 11:21 AM, Richard M. Heiberger r...@temple.edu wrote: one of my students just download mac mavericks. starting with the new system, R-3.0.1 in the APP is misbehaving. enter TRUE - FALSE (to illustrate why use of T is not a good practice) R app gives the error message invalid (do_set) left-hand side to assignment *** caught segfault *** address 0x7c0, cause 'memory not mapped' Possible actions 1 2 3 4 The R program run in the terminal behaves correctly. it reports the invalid assignment and then gives a normal R prompt. Will this happen in R-3.0.2? (yes we will download and check that). Rich, I get the same error message, but not the segfault, using 3.0.2 on Mavericks, using R.app: R version 3.0.2 (2013-09-25) -- Frisbee Sailing Copyright (C) 2013 The R Foundation for Statistical Computing Platform: x86_64-apple-darwin10.8.0 (64-bit) ... [R.app GUI 1.62 (6558) x86_64-apple-darwin10.8.0] which I otherwise never use. TRUE - FALSE Error in TRUE - FALSE : invalid (do_set) left-hand side to assignment Regards, Marc Schwartz ___ R-SIG-Mac mailing list R-SIG-Mac@r-project.org https://stat.ethz.ch/mailman/listinfo/r-sig-mac
Re: [R-SIG-Mac] mac mavericks problem
On 24 Oct 2013, at 17:37, Marc Schwartz marc_schwa...@me.com wrote: Rich, I get the same error message, but not the segfault, using 3.0.2 on Mavericks, using R.app: R version 3.0.2 (2013-09-25) -- Frisbee Sailing Copyright (C) 2013 The R Foundation for Statistical Computing Platform: x86_64-apple-darwin10.8.0 (64-bit) ... [R.app GUI 1.62 (6558) x86_64-apple-darwin10.8.0] which I otherwise never use. TRUE - FALSE Error in TRUE - FALSE : invalid (do_set) left-hand side to assignment On Mountain Lion, R 3.0.2: TRUE = FALSE Error in TRUE = FALSE : invalid (do_set) left-hand side to assignment in R.app, and in a terminal. I also get the same on a linux machine. I think that's a feature, not a bug. BW F signature.asc Description: Message signed with OpenPGP using GPGMail ___ R-SIG-Mac mailing list R-SIG-Mac@r-project.org https://stat.ethz.ch/mailman/listinfo/r-sig-mac
Re: [R-SIG-Mac] mac mavericks problem
On Oct 24, 2013, at 12:46, Federico Calboli f.calb...@imperial.ac.uk wrote: On 24 Oct 2013, at 17:37, Marc Schwartz marc_schwa...@me.com wrote: Rich, I get the same error message, but not the segfault, using 3.0.2 on Mavericks, using R.app: R version 3.0.2 (2013-09-25) -- Frisbee Sailing Copyright (C) 2013 The R Foundation for Statistical Computing Platform: x86_64-apple-darwin10.8.0 (64-bit) ... [R.app GUI 1.62 (6558) x86_64-apple-darwin10.8.0] which I otherwise never use. TRUE - FALSE Error in TRUE - FALSE : invalid (do_set) left-hand side to assignment On Mountain Lion, R 3.0.2: TRUE = FALSE Error in TRUE = FALSE : invalid (do_set) left-hand side to assignment in R.app, and in a terminal. I also get the same on a linux machine. I think that's a feature, not a bug. The error is expected; it's the (occasional) ensuing segfault which is worrisome. Michael ___ R-SIG-Mac mailing list R-SIG-Mac@r-project.org https://stat.ethz.ch/mailman/listinfo/r-sig-mac
Re: [R-SIG-Mac] mac mavericks problem
of course you never use it. it won't work. the point of the email is that writing an invalid statement should trigger only an error message. It should not trigger the segfault. It looks like the segfault is specific to 3.0.1 since your and Marc both report that you don't see the segfault on 3.0.2 I will tell the student to upgrade to 3.0.2 immediately. On Thu, Oct 24, 2013 at 12:46 PM, Federico Calboli f.calb...@imperial.ac.uk wrote: On 24 Oct 2013, at 17:37, Marc Schwartz marc_schwa...@me.com wrote: Rich, I get the same error message, but not the segfault, using 3.0.2 on Mavericks, using R.app: R version 3.0.2 (2013-09-25) -- Frisbee Sailing Copyright (C) 2013 The R Foundation for Statistical Computing Platform: x86_64-apple-darwin10.8.0 (64-bit) ... [R.app GUI 1.62 (6558) x86_64-apple-darwin10.8.0] which I otherwise never use. TRUE - FALSE Error in TRUE - FALSE : invalid (do_set) left-hand side to assignment On Mountain Lion, R 3.0.2: TRUE = FALSE Error in TRUE = FALSE : invalid (do_set) left-hand side to assignment in R.app, and in a terminal. I also get the same on a linux machine. I think that's a feature, not a bug. BW F ___ R-SIG-Mac mailing list R-SIG-Mac@r-project.org https://stat.ethz.ch/mailman/listinfo/r-sig-mac
Re: [R-SIG-Mac] mac mavericks problem
Rich, Just for clarification, I was referring to never using R.app, since I use ESS. Of course, I don't use the assignment statement either... :-) Regards, Marc On Oct 24, 2013, at 11:56 AM, Richard M. Heiberger r...@temple.edu wrote: of course you never use it. it won't work. the point of the email is that writing an invalid statement should trigger only an error message. It should not trigger the segfault. It looks like the segfault is specific to 3.0.1 since your and Marc both report that you don't see the segfault on 3.0.2 I will tell the student to upgrade to 3.0.2 immediately. On Thu, Oct 24, 2013 at 12:46 PM, Federico Calboli f.calb...@imperial.ac.uk wrote: On 24 Oct 2013, at 17:37, Marc Schwartz marc_schwa...@me.com wrote: Rich, I get the same error message, but not the segfault, using 3.0.2 on Mavericks, using R.app: R version 3.0.2 (2013-09-25) -- Frisbee Sailing Copyright (C) 2013 The R Foundation for Statistical Computing Platform: x86_64-apple-darwin10.8.0 (64-bit) ... [R.app GUI 1.62 (6558) x86_64-apple-darwin10.8.0] which I otherwise never use. TRUE - FALSE Error in TRUE - FALSE : invalid (do_set) left-hand side to assignment On Mountain Lion, R 3.0.2: TRUE = FALSE Error in TRUE = FALSE : invalid (do_set) left-hand side to assignment in R.app, and in a terminal. I also get the same on a linux machine. I think that's a feature, not a bug. BW F ___ 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
Re: [R-SIG-Mac] mac mavericks problem
To clarify, I think the issue is that R.app from 3.0.1 crashes on this error (and maybe any error) on Mavericks for the temple.edu student. We need to see if 3.0.2 does so too, but I see no change in the code which would lead me to expect a difference. On 24/10/2013 17:46, Federico Calboli wrote: On 24 Oct 2013, at 17:37, Marc Schwartz marc_schwa...@me.com wrote: Rich, I get the same error message, but not the segfault, using 3.0.2 on Mavericks, using R.app: R version 3.0.2 (2013-09-25) -- Frisbee Sailing Copyright (C) 2013 The R Foundation for Statistical Computing Platform: x86_64-apple-darwin10.8.0 (64-bit) ... [R.app GUI 1.62 (6558) x86_64-apple-darwin10.8.0] which I otherwise never use. TRUE - FALSE Error in TRUE - FALSE : invalid (do_set) left-hand side to assignment On Mountain Lion, R 3.0.2: TRUE = FALSE Error in TRUE = FALSE : invalid (do_set) left-hand side to assignment in R.app, and in a terminal. I also get the same on a linux machine. I think that's a feature, not a bug. BW F ___ R-SIG-Mac mailing list R-SIG-Mac@r-project.org https://stat.ethz.ch/mailman/listinfo/r-sig-mac -- Brian D. Ripley, rip...@stats.ox.ac.uk Professor of Applied Statistics, http://www.stats.ox.ac.uk/~ripley/ University of Oxford, Tel: +44 1865 272861 (self) 1 South Parks Road, +44 1865 272866 (PA) Oxford OX1 3TG, UKFax: +44 1865 272595 ___ R-SIG-Mac mailing list R-SIG-Mac@r-project.org https://stat.ethz.ch/mailman/listinfo/r-sig-mac
Re: [R-SIG-Mac] Updating to Mavericks
On Oct 24, 2013, at 6:16 PM, Kevin Ushey wrote: With XCode 5.0, clang is now the default compiler toolchain supplied, and llvm-gcc-4.2 is no longer available. FWIW, I and many others have had a lot of success compiling packages with the version of clang supplied with XCode. The only requirement (at this point) is that you set your own ~/.R/Makevars settings, as discussed in the SO posts -- in particular, you need CC=clang CXX=clang++ You may need to reinstall packages from source that your packages link to (e.g., Rcpp) and compile them with the new set of compilers for them to play nicely together, but in general this should work. However, hopefully others can give advice on the 'recommended' compiler toolchain now for R and Mavericks. The recommended toolchain as far as CRAN binaries are concerned remains the same since the binaries did not change. I cannot currently check on my 10.9 machine so I'll have to confirm it later, but there are several options - you can install Apple's original llvm-gcc package or use our gcc build (which includes gfortran). Depending on the route you take, you can also simply symlink the compiler to lvm-g*-4.2 instead of modifying Makevars. If you want to start from scratch (i.e. compile R and packages from sources), then you can use clang, it's known to work (modulo a few packages that are not up to date). Cheers, Simon -Kevin On Thu, Oct 24, 2013 at 3:00 PM, David Winsemius dwinsem...@comcast.net wrote: From comments made on the thread regarding the segfault in the R.app GUI following the error from TRUE - FALSE, I'm inferring that at least three people ( Prof. Ripley, S. Urbanek, and T. Bates) have installed R 3.0.2 on Mavericks. I have R version 3.0.2 (2013-09-25) -- Frisbee Sailing with R.app GUI 1.60 (6475) and XCode Version 3.2.6 in OSX 10.7.5 and have installed the Command Line Tools, so at the moment I'm generally succeeding when compiling from source. (I see I am rather behind the current GUI version although that was not my intention when I updated to 3.0.2.) Are there any specific steps one needs to take (or avoid taking) in order to preserve access to (or gain updated access to) tools for compiling packages from source? (I've seen people posting problems on SO where the error after updating to Mavericks was a missing copy of llvm-gcc-4.2.) -- David Winsemius Alameda, CA, USA ___ 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
[R-SIG-Mac] Problems installing igraph
I have an OS X 10.8.4 system, with R (3.0.2) installed and managed by macports. When I try to install the igraph package in R, I'm getting an error finding _colamd_printf installing to /Users/steevmi1/Library/R/3.0/library/igraph/libs ** R ** demo ** inst ** preparing package for lazy loading ** help *** installing help indices ** building package indices ** testing if installed package can be loaded Error : .onLoad failed in loadNamespace() for 'igraph', details: call: dyn.load(file, DLLpath = DLLpath, ...) error: unable to load shared object '/Users/steevmi1/Library/R/3.0/library/igraph/libs/igraph.so': dlopen(/Users/steevmi1/Library/R/3.0/library/igraph/libs/igraph.so, 10): Symbol not found: _colamd_printf Referenced from: /Users/steevmi1/Library/R/3.0/library/igraph/libs/igraph.so Expected in: flat namespace in /Users/steevmi1/Library/R/3.0/library/igraph/libs/igraph.so Error: loading failed Execution halted ERROR: loading failed I haven't found anything on this in google, so I'm not really sure where to go trying to track this problem down. sessionInfo() R version 3.0.2 (2013-09-25) Platform: x86_64-apple-darwin12.4.0 (64-bit) 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] tcltk_3.0.2 tools_3.0.2 -Mike -- Michael Steeves stee...@raingods.net ___ R-SIG-Mac mailing list R-SIG-Mac@r-project.org https://stat.ethz.ch/mailman/listinfo/r-sig-mac
