Re: [R-SIG-Mac] memory race
In case it helps with diagnosis: I don't replicate this behaviour on my system, running OSX 10.6.5 and R 2.11.1. I also updated to R 2.12.0 and still failed to replicate the reported behaviour. On Sun, Nov 14, 2010 at 7:09 PM, steven mosher mosherste...@gmail.com wrote: I recently started getting what I can best describe as a memory race condition in my R ( OSX 10..5.8) It started a while back with R2.11, so I upgraded to 2.12 and have the same issue System Updates have been installed. Then 2.12 was installed. Updates for X11 installed. The phenomena appears like this. Starting R (64bit) from the R.app icon R launches and consumes roughly 50mb of memory. If I open a script and merely highlight text in that window the memory consumption runs up to 1.3Gb and the system grinds to a halt. I even lose window focus temporarily. After a few minutes the memory is released and I get cursor control back. Then it will race again, Running R from the terminal R --vanilla did not exhibit these issues. Any ideas? [[alternative HTML version deleted]] ___ R-SIG-Mac mailing list R-SIG-Mac@stat.math.ethz.ch https://stat.ethz.ch/mailman/listinfo/r-sig-mac ___ R-SIG-Mac mailing list R-SIG-Mac@stat.math.ethz.ch https://stat.ethz.ch/mailman/listinfo/r-sig-mac
Re: [R-SIG-Mac] memory race
Just to add my details R version 2.12.0 (2010-10-15) Copyright (C) 2010 The R Foundation for Statistical Computing ISBN 3-900051-07-0 Platform: x86_64-apple-darwin9.8.0/x86_64 (64-bit) R is free software and comes with ABSOLUTELY NO WARRANTY. You are welcome to redistribute it under certain conditions. Type 'license()' or 'licence()' for distribution details. Natural language support but running in an English locale R is a collaborative project with many contributors. Type 'contributors()' for more information and 'citation()' on how to cite R or R packages in publications. Type 'demo()' for some demos, 'help()' for on-line help, or 'help.start()' for an HTML browser interface to help. Type 'q()' to quit R. [R.app GUI 1.35 (5632) x86_64-apple-darwin9.8.0] [History restored from /Users/mosher/.Rhistory] sessionInfo() R version 2.12.0 (2010-10-15) Platform: x86_64-apple-darwin9.8.0/x86_64 (64-bit) locale: [1] en_US.UTF-8/en_US.UTF-8/C/C/en_US.UTF-8/en_US.UTF-8 attached base packages: [1] stats graphics grDevices utils datasets methods base On Sun, Nov 14, 2010 at 3:20 PM, Mike Lawrence mike.lawre...@dal.ca wrote: In case it helps with diagnosis: I don't replicate this behaviour on my system, running OSX 10.6.5 and R 2.11.1. I also updated to R 2.12.0 and still failed to replicate the reported behaviour. On Sun, Nov 14, 2010 at 7:09 PM, steven mosher mosherste...@gmail.com wrote: I recently started getting what I can best describe as a memory race condition in my R ( OSX 10..5.8) It started a while back with R2.11, so I upgraded to 2.12 and have the same issue System Updates have been installed. Then 2.12 was installed. Updates for X11 installed. The phenomena appears like this. Starting R (64bit) from the R.app icon R launches and consumes roughly 50mb of memory. If I open a script and merely highlight text in that window the memory consumption runs up to 1.3Gb and the system grinds to a halt. I even lose window focus temporarily. After a few minutes the memory is released and I get cursor control back. Then it will race again, Running R from the terminal R --vanilla did not exhibit these issues. Any ideas? [[alternative HTML version deleted]] ___ R-SIG-Mac mailing list R-SIG-Mac@stat.math.ethz.ch https://stat.ethz.ch/mailman/listinfo/r-sig-mac [[alternative HTML version deleted]] ___ R-SIG-Mac mailing list R-SIG-Mac@stat.math.ethz.ch https://stat.ethz.ch/mailman/listinfo/r-sig-mac
Re: [R-SIG-Mac] memory race
Hi, On Sun, Nov 14, 2010 at 6:09 PM, steven mosher mosherste...@gmail.com wrote: I recently started getting what I can best describe as a memory race condition in my R snip Running R from the terminal R --vanilla did not exhibit these issues. Maybe you have some ghost data file that are being loaded on R startup? Look to see if there is a file named .RData in your home directory. What do you see when you run this command from the terminal? $ ls -ald ~/.R* If you see an .RData file there, either delete it, or rename it to something else since R will try to load this file if it finds it there (unless you start R with --vanilla, or --no-restore-data) -steve -- Steve Lianoglou Graduate Student: Computational Systems Biology | Memorial Sloan-Kettering Cancer Center | Weill Medical College of Cornell University Contact Info: http://cbio.mskcc.org/~lianos/contact ___ R-SIG-Mac mailing list R-SIG-Mac@stat.math.ethz.ch https://stat.ethz.ch/mailman/listinfo/r-sig-mac
Re: [R-SIG-Mac] memory race
Hi, Don't forget to cc r-sig-mac to keep correspondence, you'll likely get quicker + more informed suggestions if the whole community can see what's going on. On Sun, Nov 14, 2010 at 9:30 PM, steven mosher mosherste...@gmail.com wrote: It sure looks like it is trying to access a file or something. The problem may have started when I was accessing some large files. is it possible there is a connection open I'm guessing not ... weird that `R --vanilla` worked for a bit, then stopped. Also, these errors from another email sent earlier: dyld: lazy symbol binding failed: Symbol not found: _iconv_open Referenced from: /Library/Frameworks/R.framework/Resources/lib/i386/libR.dylib Expected in: /sw/lib/libiconv.2.dylib dyld: Symbol not found: _iconv_open Referenced from: /Library/Frameworks/R.framework/Resources/lib/i386/libR.dylib Expected in: /sw/lib/libiconv.2.dylib It's weird that R is fishing into your fink install for something ... maybe someone else will be able to make some sense out of it. -steve -- Steve Lianoglou Graduate Student: Computational Systems Biology | Memorial Sloan-Kettering Cancer Center | Weill Medical College of Cornell University Contact Info: http://cbio.mskcc.org/~lianos/contact ___ R-SIG-Mac mailing list R-SIG-Mac@stat.math.ethz.ch https://stat.ethz.ch/mailman/listinfo/r-sig-mac
Re: [R-SIG-Mac] memory race
weirdly my R stopped working altogether R version 2.12.0 (2010-10-15) Copyright (C) 2010 The R Foundation for Statistical Computing ISBN 3-900051-07-0 Platform: i386-apple-darwin9.8.0/i386 (32-bit) R is free software and comes with ABSOLUTELY NO WARRANTY. You are welcome to redistribute it under certain conditions. Type 'license()' or 'licence()' for distribution details. dyld: lazy symbol binding failed: Symbol not found: _iconv_open Referenced from: /Library/Frameworks/R.framework/Resources/lib/i386/libR.dylib Expected in: /sw/lib/libiconv.2.dylib dyld: Symbol not found: _iconv_open Referenced from: /Library/Frameworks/R.framework/Resources/lib/i386/libR.dylib Expected in: /sw/lib/libiconv.2.dylib On Sun, Nov 14, 2010 at 5:41 PM, Steve Lianoglou mailinglist.honey...@gmail.com wrote: Hi, On Sun, Nov 14, 2010 at 6:09 PM, steven mosher mosherste...@gmail.com wrote: I recently started getting what I can best describe as a memory race condition in my R snip Running R from the terminal R --vanilla did not exhibit these issues. Maybe you have some ghost data file that are being loaded on R startup? Look to see if there is a file named .RData in your home directory. What do you see when you run this command from the terminal? $ ls -ald ~/.R* If you see an .RData file there, either delete it, or rename it to something else since R will try to load this file if it finds it there (unless you start R with --vanilla, or --no-restore-data) -steve -- Steve Lianoglou Graduate Student: Computational Systems Biology | Memorial Sloan-Kettering Cancer Center | Weill Medical College of Cornell University Contact Info: http://cbio.mskcc.org/~lianos/contacthttp://cbio.mskcc.org/%7Elianos/contact [[alternative HTML version deleted]] ___ R-SIG-Mac mailing list R-SIG-Mac@stat.math.ethz.ch https://stat.ethz.ch/mailman/listinfo/r-sig-mac
Re: [R-SIG-Mac] memory race
I've had nothing but trouble with fink. Nit sure why R stopped working, but the memory race is 100% repeatable for me. Any attempt to open a script leads to a race. It gobbles up 1.4Gb and then sits there. Then the memory use drops back to 50mb. everything works fine in the console but if I use the UI to touch any file its a 2 minute wait. On Sun, Nov 14, 2010 at 8:33 PM, Steve Lianoglou mailinglist.honey...@gmail.com wrote: Hi, Don't forget to cc r-sig-mac to keep correspondence, you'll likely get quicker + more informed suggestions if the whole community can see what's going on. On Sun, Nov 14, 2010 at 9:30 PM, steven mosher mosherste...@gmail.com wrote: It sure looks like it is trying to access a file or something. The problem may have started when I was accessing some large files. is it possible there is a connection open I'm guessing not ... weird that `R --vanilla` worked for a bit, then stopped. Also, these errors from another email sent earlier: dyld: lazy symbol binding failed: Symbol not found: _iconv_open Referenced from: /Library/Frameworks/R.framework/Resources/lib/i386/libR.dylib Expected in: /sw/lib/libiconv.2.dylib dyld: Symbol not found: _iconv_open Referenced from: /Library/Frameworks/R.framework/Resources/lib/i386/libR.dylib Expected in: /sw/lib/libiconv.2.dylib It's weird that R is fishing into your fink install for something ... maybe someone else will be able to make some sense out of it. -steve -- Steve Lianoglou Graduate Student: Computational Systems Biology | Memorial Sloan-Kettering Cancer Center | Weill Medical College of Cornell University Contact Info: http://cbio.mskcc.org/~lianos/contacthttp://cbio.mskcc.org/%7Elianos/contact [[alternative HTML version deleted]] ___ R-SIG-Mac mailing list R-SIG-Mac@stat.math.ethz.ch https://stat.ethz.ch/mailman/listinfo/r-sig-mac
