Re: [R] R 2.8.1 and 2.9 alpha crash when running survest of Design package
The Design package is incompatible with updates to the survival package (version 2.35 and higher) that were made for version 2.9.0. It calls some internal fitting functions (coxreg.fit, agreg.fit) whose arguments have changed. According to the CRAN checks, about a dozen other packages were also affected by other changes in the update, but most just give an error message rather than crash. Maintainers of all the packages have been notified and given my best guess at the reason for their specific incompatibility (and an offer of further assistance if necessary) You may need to downgrade to version 2.34 of the survival package until Design is updated. -thomas On Fri, 27 Mar 2009, Nguyen Dinh Nguyen wrote: Dear Prof Harrell and everyone, My PC: Window XP service pack 3 and service pack 2 R version 2.8.1 and 2.9 alpha For the last 3 days, after updating R, my two computers have been facing problems when running existing and runable R commands that involves with Design package I attempt to use 'survest', but I failed all the times with R (both 2.8.1 and 2.9 alpha) being shut down immediately with following error report messages. AppName: rgui.exe AppVer: 2.90.48212.0 ModName: survival.dll ModVer: 0.0.0.0 Offset: 7749 However, if I run these commands on other computers which have not been updated for 2 week, they run OK Could you please consider the matter and give me advice I am looking forward to hearing from you soon Regards Nguyen D Nguyen Garvan Institute of Medical Research Sydney, Australia [[alternative HTML version deleted]] __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code. Thomas Lumley Assoc. Professor, Biostatistics tlum...@u.washington.eduUniversity of Washington, Seattle __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
Re: [R] R 2.8.1 and 2.9 alpha crash when running survest of Design package
A couple additions to Thomas's message. The 'survest' function in design directly called C routines in the survival package. The argument list to the routines changed due to the addition of weights; calling a C routine with the wrong arguments is one of the more reliable ways to crash a program. The simplest (short term) solution is to use survfit for your curves rather than survest. Frank Harrell has been aware of the issue for several weeks and is working hard on solving it. The simple fix is a few minutes, but he's thinking about how to avoid any future problems. The C routines in survival change arguments VERY rarely, but direcly calling the routines of another package is considered dangerous in general. Most breakage was less severe. For instance there were a couple of errors in the PBC data set. I fixed these, and also replaced all the 999 codes with NA to make it easier to use. Some other packages use this data. (My name is on most of the PBC papers and I have the master PBC data with all labs, patient id, etc, but I was not the source of the first data set). We'll be keeping an eye on the R list as the package rolls out; sending a message directly to Thomas and/or I would also be appreciated for issues like this. Terry Therneau __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
Re: [R] R 2.8.1 and 2.9 alpha crash when running survest of Design package
We will try to quickly get out a new version of Design that checks for the version of survival that is installed and uses a different .C call accordingly. This will involve ignoring (for now) the new weights option Terry has implemented. Frank Terry Therneau wrote: A couple additions to Thomas's message. The 'survest' function in design directly called C routines in the survival package. The argument list to the routines changed due to the addition of weights; calling a C routine with the wrong arguments is one of the more reliable ways to crash a program. The simplest (short term) solution is to use survfit for your curves rather than survest. Frank Harrell has been aware of the issue for several weeks and is working hard on solving it. The simple fix is a few minutes, but he's thinking about how to avoid any future problems. The C routines in survival change arguments VERY rarely, but direcly calling the routines of another package is considered dangerous in general. Most breakage was less severe. For instance there were a couple of errors in the PBC data set. I fixed these, and also replaced all the 999 codes with NA to make it easier to use. Some other packages use this data. (My name is on most of the PBC papers and I have the master PBC data with all labs, patient id, etc, but I was not the source of the first data set). We'll be keeping an eye on the R list as the package rolls out; sending a message directly to Thomas and/or I would also be appreciated for issues like this. Terry Therneau __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code. -- Frank E Harrell Jr Professor and Chair School of Medicine Department of Biostatistics Vanderbilt University __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
