Can anyone suggest what I may be doing wrong? I had issued the command update.packages(), after which I went through the usual dialog: mixtools : Version 0.2.0 installed in /Library/Frameworks/R.framework/Resources/ library Version 0.3.0 available at http://lib.stat.cmu.edu/R/CRAN Update (y/N/c)? y ? tsDyn : Version 0.5-7 installed in /Library/Frameworks/R.framework/Resources/ library Version 0.6-0 available at http://lib.stat.cmu.edu/R/CRAN Update (y/N/c)? y trying URL 'http://lib.stat.cmu.edu/R/CRAN/bin/macosx/universal/contrib/2.6/mixtools_0.3.0.tgz' Content type 'application/x-gzip' length 325712 bytes (318 Kb) opened URL ================================================== downloaded 318 Kb ? trying URL 'http://lib.stat.cmu.edu/R/CRAN/bin/macosx/universal/contrib/2.6/tsDyn_0.6-0.tgz' Content type 'application/x-gzip' length 519954 bytes (507 Kb) opened URL ================================================== downloaded 507 Kb *** caught bus error *** address 0x20, cause 'non-existent physical address' Traceback: 1: unlink(instPath, recursive = TRUE) 2: unpackPkg(foundpkgs[okp, 2], foundpkgs[okp, 1], lib, installWithVers) 3: .install.macbinary(pkgs = pkgs, lib = lib, contriburl = contriburl, method = method, available = available, destdir = destdir, installWithVers = installWithVers, dependencies = dependencies) 4: install.packages(update[instlib == l, "Package"], l, contriburl = contriburl, method = method, available = available, ..., type = type) 5: update.packages() I am running R version 2.6.1 (2007-11-26) i386-apple-darwin8.10.1 locale: 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 _____________________________ Professor Michael Kubovy University of Virginia Department of Psychology USPS: P.O.Box 400400 Charlottesville, VA 22904-4400 Parcels: Room 102 Gilmer Hall McCormick Road Charlottesville, VA 22903 Office: B011 +1-434-982-4729 Lab: B019 +1-434-982-4751 Fax: +1-434-982-4766 WWW: http://www.people.virginia.edu/~mk9y/
Bus error while updating packages
5 messages · Michael Kubovy, Simon Urbanek, Erich Neuwirth
Michael, can you, please, send me a full stack trace (i.e. run R with "R -d gdb" then type "c", do whatever it takes to crash R, type "bt" and send me the result). Unfortunately I'm not able to reproduce this myself, but it has occurred before to other users. Thanks, Simon
On Feb 7, 2008, at 9:58 PM, Michael Kubovy wrote:
Can anyone suggest what I may be doing wrong? I had issued the command update.packages(), after which I went through the usual dialog: mixtools : Version 0.2.0 installed in /Library/Frameworks/R.framework/Resources/ library Version 0.3.0 available at http://lib.stat.cmu.edu/R/CRAN Update (y/N/c)? y ? tsDyn : Version 0.5-7 installed in /Library/Frameworks/R.framework/Resources/ library Version 0.6-0 available at http://lib.stat.cmu.edu/R/CRAN Update (y/N/c)? y trying URL 'http://lib.stat.cmu.edu/R/CRAN/bin/macosx/universal/contrib/2.6/mixtools_0.3.0.tgz' Content type 'application/x-gzip' length 325712 bytes (318 Kb) opened URL ================================================== downloaded 318 Kb ? trying URL 'http://lib.stat.cmu.edu/R/CRAN/bin/macosx/universal/contrib/2.6/tsDyn_0.6-0.tgz' Content type 'application/x-gzip' length 519954 bytes (507 Kb) opened URL ================================================== downloaded 507 Kb *** caught bus error *** address 0x20, cause 'non-existent physical address' Traceback: 1: unlink(instPath, recursive = TRUE) 2: unpackPkg(foundpkgs[okp, 2], foundpkgs[okp, 1], lib, installWithVers) 3: .install.macbinary(pkgs = pkgs, lib = lib, contriburl = contriburl, method = method, available = available, destdir = destdir, installWithVers = installWithVers, dependencies = dependencies) 4: install.packages(update[instlib == l, "Package"], l, contriburl = contriburl, method = method, available = available, ..., type = type) 5: update.packages() I am running R version 2.6.1 (2007-11-26) i386-apple-darwin8.10.1 locale: 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
_____________________________
Professor Michael Kubovy
University of Virginia
Department of Psychology
USPS: P.O.Box 400400 Charlottesville, VA 22904-4400
Parcels: Room 102 Gilmer Hall
McCormick Road Charlottesville, VA 22903
Office: B011 +1-434-982-4729
Lab: B019 +1-434-982-4751
Fax: +1-434-982-4766
WWW: http://www.people.virginia.edu/~mk9y/
_______________________________________________
R-SIG-Mac mailing list
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I know this question belongs to this list only to 50 percent ;-) I finally managed to install R 2.5.1 (on Leopard) and should be able to use R from within SPSS with SPSS plugin. My problem ist that whenever I do a print or a cat in an "embedded" R program, SPSS crashes. Does anybody on this list have experience with the SPSS-R combination on Leopard? Has somebody else experienced similar problems?
Erich Neuwirth, University of Vienna Faculty of Computer Science Computer Supported Didactics Working Group Visit our SunSITE at http://sunsite.univie.ac.at Phone: +43-1-4277-39464 Fax: +43-1-4277-39459
I think I have traced the bug. It's fixed in 2.6.2 patched, but also just in time for the Mac 2.6.2 CRAN binary released today. Cheers, Simon
On Feb 7, 2008, at 9:58 PM, Michael Kubovy wrote:
Can anyone suggest what I may be doing wrong? I had issued the command update.packages(), after which I went through the usual dialog: mixtools : Version 0.2.0 installed in /Library/Frameworks/R.framework/Resources/ library Version 0.3.0 available at http://lib.stat.cmu.edu/R/CRAN Update (y/N/c)? y ? tsDyn : Version 0.5-7 installed in /Library/Frameworks/R.framework/Resources/ library Version 0.6-0 available at http://lib.stat.cmu.edu/R/CRAN Update (y/N/c)? y trying URL 'http://lib.stat.cmu.edu/R/CRAN/bin/macosx/universal/contrib/2.6/mixtools_0.3.0.tgz' Content type 'application/x-gzip' length 325712 bytes (318 Kb) opened URL ================================================== downloaded 318 Kb ? trying URL 'http://lib.stat.cmu.edu/R/CRAN/bin/macosx/universal/contrib/2.6/tsDyn_0.6-0.tgz' Content type 'application/x-gzip' length 519954 bytes (507 Kb) opened URL ================================================== downloaded 507 Kb *** caught bus error *** address 0x20, cause 'non-existent physical address' Traceback: 1: unlink(instPath, recursive = TRUE) 2: unpackPkg(foundpkgs[okp, 2], foundpkgs[okp, 1], lib, installWithVers) 3: .install.macbinary(pkgs = pkgs, lib = lib, contriburl = contriburl, method = method, available = available, destdir = destdir, installWithVers = installWithVers, dependencies = dependencies) 4: install.packages(update[instlib == l, "Package"], l, contriburl = contriburl, method = method, available = available, ..., type = type) 5: update.packages() I am running R version 2.6.1 (2007-11-26) i386-apple-darwin8.10.1 locale: 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
_____________________________
Professor Michael Kubovy
University of Virginia
Department of Psychology
USPS: P.O.Box 400400 Charlottesville, VA 22904-4400
Parcels: Room 102 Gilmer Hall
McCormick Road Charlottesville, VA 22903
Office: B011 +1-434-982-4729
Lab: B019 +1-434-982-4751
Fax: +1-434-982-4766
WWW: http://www.people.virginia.edu/~mk9y/
_______________________________________________
R-SIG-Mac mailing list
R-SIG-Mac at stat.math.ethz.ch
https://stat.ethz.ch/mailman/listinfo/r-sig-mac
1 day later
Afert completely removing all versions of R, reinstalling them in historical order, and reinstalling the R plugin in SPSS things finally work as they should.
Erich Neuwirth wrote:
I know this question belongs to this list only to 50 percent ;-) I finally managed to install R 2.5.1 (on Leopard) and should be able to use R from within SPSS with SPSS plugin. My problem ist that whenever I do a print or a cat in an "embedded" R program, SPSS crashes. Does anybody on this list have experience with the SPSS-R combination on Leopard? Has somebody else experienced similar problems?
Erich Neuwirth, University of Vienna Faculty of Computer Science Computer Supported Didactics Working Group Visit our SunSITE at http://sunsite.univie.ac.at Phone: +43-1-4277-39464 Fax: +43-1-4277-39459