Re: [R-SIG-Mac] Unload CRAN package and locally built package
Hi Simon, thanks for the answer, sorry, I should have included this, it is apparently not in sessionInfo(). So, this happens on 10.9.4 with R 3.1.1 and also on 10.8.5 with R 3.1.0. And the (10.8) CRAN binary version of igraph unloads cleanly on both of them. I am not sure how and why destructors would be called when unloading, igraph does not use any external pointers to keep C++ objects alive. They should be destroyed when returning the C/C++ call to R. It is certainly possible that they are not, because of a bug or something, but I cannot even unload if I do not call any igraph functions at all, just load the package. (Loading the package calls an igraph_init, but that only sets some global variables, it does not create any C or C++ objects.) But I definitely think that you are right in general, and this is some binary incompatibility between the R binary and my binary. It has been a long standing issue, actually. It never worked for me in the last ~5 years. I am also not really sure how to debug this, but will check with an R version compiled on my mac in a minute. Thank again, Best, Gabor On Thu, Sep 25, 2014 at 10:53 PM, Simon Urbanek simon.urba...@r-project.org wrote: Gabor, what OS X version are you using? More recent OS X versions have slightly different C++ ABI so you can't really mix C++ code compiled on SL and let's say Mavericks - hence the two different sets of binaries. That would be my guess here since igraph uses C++ and it involves destructor code on unloading... Cheers, Simon On Sep 25, 2014, at 11:27 AM, Gábor Csárdi csardi.ga...@gmail.com wrote: Hi all, I have a little mystery here, and ideas would be welcome. I would like to unload the package igraph. The following works fine with the package downloaded from CRAN (Snow Leopard package): install.packages(igraph) library(igraph) library(devtools) unload(inst(igraph)) However, if I build the package myself on my machine, then it does not work any more and unloading hangs. I can press CTRL+C to get the R prompt back, but every command hangs again. This is my machine: ~$ xcodebuild -version Xcode 5.1.1 Build version 5B1008 ~$ Rscript -e 'sessionInfo()' R version 3.1.1 (2014-07-10) Platform: x86_64-apple-darwin10.8.0 (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 base It also hangs if I call dyn.unload() directly, instead of calling devtools; if I remove the igraph.so file from the package, then it works again, so it is definitely something with the .so file. I know this is not much work with, but if you have any guesses, please let me know. Thanks, Gabor ___ 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] Unload CRAN package and locally built package
I just tried on an R version that I compiled myself, and unloading works fine. \o/ I also tried using the Mavericks build of R, and that works fine, too, on my Mavericks laptop. \o/ I have no idea why the Snow Leopard R build did not work with my other Snow Leopard machine, but honestly, I don't care much about it. :) Thanks for the help, this is already a great day, and it is only 5:50am! :) Best, Gabor On Fri, Sep 26, 2014 at 4:40 AM, Gábor Csárdi csardi.ga...@gmail.com wrote: Hi Simon, thanks for the answer, sorry, I should have included this, it is apparently not in sessionInfo(). So, this happens on 10.9.4 with R 3.1.1 and also on 10.8.5 with R 3.1.0. And the (10.8) CRAN binary version of igraph unloads cleanly on both of them. I am not sure how and why destructors would be called when unloading, igraph does not use any external pointers to keep C++ objects alive. They should be destroyed when returning the C/C++ call to R. It is certainly possible that they are not, because of a bug or something, but I cannot even unload if I do not call any igraph functions at all, just load the package. (Loading the package calls an igraph_init, but that only sets some global variables, it does not create any C or C++ objects.) But I definitely think that you are right in general, and this is some binary incompatibility between the R binary and my binary. It has been a long standing issue, actually. It never worked for me in the last ~5 years. I am also not really sure how to debug this, but will check with an R version compiled on my mac in a minute. Thank again, Best, Gabor On Thu, Sep 25, 2014 at 10:53 PM, Simon Urbanek simon.urba...@r-project.org wrote: Gabor, what OS X version are you using? More recent OS X versions have slightly different C++ ABI so you can't really mix C++ code compiled on SL and let's say Mavericks - hence the two different sets of binaries. That would be my guess here since igraph uses C++ and it involves destructor code on unloading... Cheers, Simon On Sep 25, 2014, at 11:27 AM, Gábor Csárdi csardi.ga...@gmail.com wrote: Hi all, I have a little mystery here, and ideas would be welcome. I would like to unload the package igraph. The following works fine with the package downloaded from CRAN (Snow Leopard package): install.packages(igraph) library(igraph) library(devtools) unload(inst(igraph)) However, if I build the package myself on my machine, then it does not work any more and unloading hangs. I can press CTRL+C to get the R prompt back, but every command hangs again. This is my machine: ~$ xcodebuild -version Xcode 5.1.1 Build version 5B1008 ~$ Rscript -e 'sessionInfo()' R version 3.1.1 (2014-07-10) Platform: x86_64-apple-darwin10.8.0 (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 base It also hangs if I call dyn.unload() directly, instead of calling devtools; if I remove the igraph.so file from the package, then it works again, so it is definitely something with the .so file. I know this is not much work with, but if you have any guesses, please let me know. Thanks, Gabor ___ 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] Unload CRAN package and locally built package
Hi all, I have a little mystery here, and ideas would be welcome. I would like to unload the package igraph. The following works fine with the package downloaded from CRAN (Snow Leopard package): install.packages(igraph) library(igraph) library(devtools) unload(inst(igraph)) However, if I build the package myself on my machine, then it does not work any more and unloading hangs. I can press CTRL+C to get the R prompt back, but every command hangs again. This is my machine: ~$ xcodebuild -version Xcode 5.1.1 Build version 5B1008 ~$ Rscript -e 'sessionInfo()' R version 3.1.1 (2014-07-10) Platform: x86_64-apple-darwin10.8.0 (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 base It also hangs if I call dyn.unload() directly, instead of calling devtools; if I remove the igraph.so file from the package, then it works again, so it is definitely something with the .so file. I know this is not much work with, but if you have any guesses, please let me know. Thanks, Gabor ___ R-SIG-Mac mailing list R-SIG-Mac@r-project.org https://stat.ethz.ch/mailman/listinfo/r-sig-mac
