Hello list, I've seen the recent discussions documenting problems with lm. I have encountered the following problem. I use WinXP Pro with service pack 1, and R 1.9.0, on a XEON 2GHz, with 1GB of RAM.> eff.frostd.dev mean NSTRDSP 7.403749e-01 1.215686e-01 CPFGEP 9.056763e+00 1.815686e+00 WSWOLF 4.703588e+05 1.112832e+05 NPILGRIM 1.017640e+06 2.134335e+05 WSNMILE 1.367312e+07 1.892021e+06 WSHIDESL 1.830811e+07 1.892021e+06> reg <- lm(log(mean) ~ log(std.dev), data=eff.fro)Error in model.matrix.default(mt, mf, contrasts) : cannot allocate vector of length 1074790452> log(eff.fro$mean)[1] -2.1072763 0.5964635 11.6198339 12.2710808 14.4531561 [6] 14.4531561> reg <- lm(log(eff.fro$mean) ~ log(eff.fro$std.dev))Error: cannot allocate vector of size 3360077 Kb> lef <- log(eff.fro) > lefstd.dev mean NSTRDSP -0.3005986 -2.1072763 CPFGEP 2.2035117 0.5964635 WSWOLF 13.0612512 11.6198339 NPILGRIM 13.8329973 12.2710808 WSNMILE 16.4309427 14.4531561 WSHIDESL 16.7228546 14.4531561> lef <- log(eff.fro) > reg <- lm(lef$mean ~ lef$std.dev)Here the my computer completely crashed. A window poped-up and said memory problem at address ..., and if I want to debug. I ran the same code one more time, and it worked but it did not work how I wanted (where is the slope?):> reg <- lm(lef$mean ~ lef$std.dev) > regCall: lm(formula = lef$mean ~ lef$std.dev) Coefficients: (Intercept) 8.548> > summary(reg)Call: lm(formula = lef$mean ~ lef$std.dev) Residuals: 1 2 3 4 5 6 -10.655 -7.951 3.072 3.723 5.905 5.905 Coefficients: Estimate Std. Error t value Pr(>|t|) (Intercept) 8.548 2.999 2.85 0.0358 * --- Signif. codes: 0 `***' 0.001 `**' 0.01 `*' 0.05 `.' 0.1 ` ' 1 Residual standard error: 7.346 on 5 degrees of freedom I ran again: reg <- lm(log(mean) ~ log(std.dev), data=eff.fro) and I get the pop-up: The instruction at "0x6b4c45a5" referenced memory at "0x0032374a". The memory could not be "read". Click OK to terminate the program. Any ideas? Thank you, Adrian
Can you show us the output of str(eff.fro)? Do you have other things in the global environment or the search path that's taking up memory? What does gc() say? Andy> From: Adrian Dragulescu > > Hello list, > > I've seen the recent discussions documenting problems with lm. > > I have encountered the following problem. I use WinXP Pro with > service pack 1, and R 1.9.0, on a XEON 2GHz, with 1GB of RAM. > > > eff.fro > std.dev mean > NSTRDSP 7.403749e-01 1.215686e-01 > CPFGEP 9.056763e+00 1.815686e+00 > WSWOLF 4.703588e+05 1.112832e+05 > NPILGRIM 1.017640e+06 2.134335e+05 > WSNMILE 1.367312e+07 1.892021e+06 > WSHIDESL 1.830811e+07 1.892021e+06 > > reg <- lm(log(mean) ~ log(std.dev), data=eff.fro) > Error in model.matrix.default(mt, mf, contrasts) : > cannot allocate vector of length 1074790452 > > log(eff.fro$mean) > [1] -2.1072763 0.5964635 11.6198339 12.2710808 14.4531561 > [6] 14.4531561 > > reg <- lm(log(eff.fro$mean) ~ log(eff.fro$std.dev)) > Error: cannot allocate vector of size 3360077 Kb > > lef <- log(eff.fro) > > lef > std.dev mean > NSTRDSP -0.3005986 -2.1072763 > CPFGEP 2.2035117 0.5964635 > WSWOLF 13.0612512 11.6198339 > NPILGRIM 13.8329973 12.2710808 > WSNMILE 16.4309427 14.4531561 > WSHIDESL 16.7228546 14.4531561 > > lef <- log(eff.fro) > > reg <- lm(lef$mean ~ lef$std.dev) > > Here the my computer completely crashed. A window poped-up and said > memory problem at address ..., and if I want to debug. > > I ran the same code one more time, and it worked but it did not work > how I wanted (where is the slope?): > > reg <- lm(lef$mean ~ lef$std.dev) > > reg > > Call: > lm(formula = lef$mean ~ lef$std.dev) > > Coefficients: > (Intercept) > 8.548 > > > > > summary(reg) > > Call: > lm(formula = lef$mean ~ lef$std.dev) > > Residuals: > 1 2 3 4 5 6 > -10.655 -7.951 3.072 3.723 5.905 5.905 > > Coefficients: > Estimate Std. Error t value Pr(>|t|) > (Intercept) 8.548 2.999 2.85 0.0358 * > --- > Signif. codes: 0 `***' 0.001 `**' 0.01 `*' 0.05 `.' 0.1 ` ' 1 > > Residual standard error: 7.346 on 5 degrees of freedom > > I ran again: > > reg <- lm(log(mean) ~ log(std.dev), data=eff.fro) > > and I get the pop-up: > The instruction at "0x6b4c45a5" referenced memory at "0x0032374a". > The memory could not be "read". Click OK to terminate the program. > > > Any ideas? Thank you, > Adrian > > ______________________________________________ > R-help at stat.math.ethz.ch mailing list > https://www.stat.math.ethz.ch/mailman/listinfo/r-help > PLEASE do read the posting guide! > http://www.R-project.org/posting-guide.html > >------------------------------------------------------------------------------ Notice: This e-mail message, together with any attachments,...{{dropped}}
This may or may not be the same problem (which is already solved). But please read the section on BUGS in the R FAQ and set up a reproducible example. Then try out the current version of r-patched (one dated tomorrow or later, to be safe) and see if the problem recurs. If it does, please file a bug report. My guess is that eff.fro$std.dev is a 1D array (use dim or str to find out), and you did not intend that. On Thu, 29 Apr 2004, Adrian Dragulescu wrote:> > Hello list, > > I've seen the recent discussions documenting problems with lm. > > I have encountered the following problem. I use WinXP Pro with > service pack 1, and R 1.9.0, on a XEON 2GHz, with 1GB of RAM. > > > eff.fro > std.dev mean > NSTRDSP 7.403749e-01 1.215686e-01 > CPFGEP 9.056763e+00 1.815686e+00 > WSWOLF 4.703588e+05 1.112832e+05 > NPILGRIM 1.017640e+06 2.134335e+05 > WSNMILE 1.367312e+07 1.892021e+06 > WSHIDESL 1.830811e+07 1.892021e+06 > > reg <- lm(log(mean) ~ log(std.dev), data=eff.fro) > Error in model.matrix.default(mt, mf, contrasts) : > cannot allocate vector of length 1074790452 > > log(eff.fro$mean) > [1] -2.1072763 0.5964635 11.6198339 12.2710808 14.4531561 > [6] 14.4531561 > > reg <- lm(log(eff.fro$mean) ~ log(eff.fro$std.dev)) > Error: cannot allocate vector of size 3360077 Kb > > lef <- log(eff.fro) > > lef > std.dev mean > NSTRDSP -0.3005986 -2.1072763 > CPFGEP 2.2035117 0.5964635 > WSWOLF 13.0612512 11.6198339 > NPILGRIM 13.8329973 12.2710808 > WSNMILE 16.4309427 14.4531561 > WSHIDESL 16.7228546 14.4531561 > > lef <- log(eff.fro) > > reg <- lm(lef$mean ~ lef$std.dev) > > Here the my computer completely crashed. A window poped-up and said > memory problem at address ..., and if I want to debug. > > I ran the same code one more time, and it worked but it did not work > how I wanted (where is the slope?): > > reg <- lm(lef$mean ~ lef$std.dev) > > reg > > Call: > lm(formula = lef$mean ~ lef$std.dev) > > Coefficients: > (Intercept) > 8.548 > > > > > summary(reg) > > Call: > lm(formula = lef$mean ~ lef$std.dev) > > Residuals: > 1 2 3 4 5 6 > -10.655 -7.951 3.072 3.723 5.905 5.905 > > Coefficients: > Estimate Std. Error t value Pr(>|t|) > (Intercept) 8.548 2.999 2.85 0.0358 * > --- > Signif. codes: 0 `***' 0.001 `**' 0.01 `*' 0.05 `.' 0.1 ` ' 1 > > Residual standard error: 7.346 on 5 degrees of freedom > > I ran again: > > reg <- lm(log(mean) ~ log(std.dev), data=eff.fro) > > and I get the pop-up: > The instruction at "0x6b4c45a5" referenced memory at "0x0032374a". > The memory could not be "read". Click OK to terminate the program. > > > Any ideas? Thank you, > Adrian > > ______________________________________________ > R-help at stat.math.ethz.ch mailing list > https://www.stat.math.ethz.ch/mailman/listinfo/r-help > PLEASE do read the posting guide! http://www.R-project.org/posting-guide.html > >-- Brian D. Ripley, ripley at 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, UK Fax: +44 1865 272595
I believe Prof. Ripley is right. The problem is> $ std.dev: num [, 1:6] 7.40e-01 9.06e+00 4.70e+05 1.02e+06 > 1.37e+07 ... > ..- attr(*, "dimnames")=List of 1which looks like an array, rather than a vector. Andy> From: Adrian Dragulescu [mailto:adrian_d at eskimo.com] > > If I enforce the variables to be numeric it works fine. > > > str(eff.fro) > `data.frame': 6 obs. of 2 variables: > $ std.dev: num [, 1:6] 7.40e-01 9.06e+00 4.70e+05 1.02e+06 > 1.37e+07 ... > ..- attr(*, "dimnames")=List of 1 > .. ..$ : chr "NSTRDSP" "CPFGEP" "WSWOLF" "NPILGRIM" ... > $ mean : num 1.22e-01 1.82e+00 1.11e+05 2.13e+05 1.89e+06 ... > > gc() > used (Mb) gc trigger (Mb) > Ncells 578941 15.5 1166886 31.2 > Vcells 589444 4.5 2377385 18.2 > > eff.fro > std.dev mean > NSTRDSP 7.403749e-01 1.215686e-01 > CPFGEP 9.056763e+00 1.815686e+00 > WSWOLF 4.703588e+05 1.112832e+05 > NPILGRIM 1.017640e+06 2.134335e+05 > WSNMILE 1.367312e+07 1.892021e+06 > WSHIDESL 1.830811e+07 1.892021e+06 > > reg <- lm(log(as.numeric(mean)) ~ log(as.numeric(std.dev)), > data=eff.fro) > > reg > > Call: > lm(formula = log(as.numeric(mean)) ~ > log(as.numeric(std.dev)), data > eff.fro) > > Coefficients: > (Intercept) log(as.numeric(std.dev)) > -1.6368 0.9864 > > > Adrian > > > On Thu, 29 Apr 2004, Liaw, Andy wrote: > > > Can you show us the output of str(eff.fro)? Do you have > other things in the > > global environment or the search path that's taking up > memory? What does > > gc() say? > > > > Andy > > > > > From: Adrian Dragulescu > > > > > > Hello list, > > > > > > I've seen the recent discussions documenting problems with lm. > > > > > > I have encountered the following problem. I use WinXP Pro with > > > service pack 1, and R 1.9.0, on a XEON 2GHz, with 1GB of RAM. > > > > > > > eff.fro > > > std.dev mean > > > NSTRDSP 7.403749e-01 1.215686e-01 > > > CPFGEP 9.056763e+00 1.815686e+00 > > > WSWOLF 4.703588e+05 1.112832e+05 > > > NPILGRIM 1.017640e+06 2.134335e+05 > > > WSNMILE 1.367312e+07 1.892021e+06 > > > WSHIDESL 1.830811e+07 1.892021e+06 > > > > reg <- lm(log(mean) ~ log(std.dev), data=eff.fro) > > > Error in model.matrix.default(mt, mf, contrasts) : > > > cannot allocate vector of length 1074790452 > > > > log(eff.fro$mean) > > > [1] -2.1072763 0.5964635 11.6198339 12.2710808 14.4531561 > > > [6] 14.4531561 > > > > reg <- lm(log(eff.fro$mean) ~ log(eff.fro$std.dev)) > > > Error: cannot allocate vector of size 3360077 Kb > > > > lef <- log(eff.fro) > > > > lef > > > std.dev mean > > > NSTRDSP -0.3005986 -2.1072763 > > > CPFGEP 2.2035117 0.5964635 > > > WSWOLF 13.0612512 11.6198339 > > > NPILGRIM 13.8329973 12.2710808 > > > WSNMILE 16.4309427 14.4531561 > > > WSHIDESL 16.7228546 14.4531561 > > > > lef <- log(eff.fro) > > > > reg <- lm(lef$mean ~ lef$std.dev) > > > > > > Here the my computer completely crashed. A window > poped-up and said > > > memory problem at address ..., and if I want to debug. > > > > > > I ran the same code one more time, and it worked but it > did not work > > > how I wanted (where is the slope?): > > > > reg <- lm(lef$mean ~ lef$std.dev) > > > > reg > > > > > > Call: > > > lm(formula = lef$mean ~ lef$std.dev) > > > > > > Coefficients: > > > (Intercept) > > > 8.548 > > > > > > > > > > > summary(reg) > > > > > > Call: > > > lm(formula = lef$mean ~ lef$std.dev) > > > > > > Residuals: > > > 1 2 3 4 5 6 > > > -10.655 -7.951 3.072 3.723 5.905 5.905 > > > > > > Coefficients: > > > Estimate Std. Error t value Pr(>|t|) > > > (Intercept) 8.548 2.999 2.85 0.0358 * > > > --- > > > Signif. codes: 0 `***' 0.001 `**' 0.01 `*' 0.05 `.' 0.1 ` ' 1 > > > > > > Residual standard error: 7.346 on 5 degrees of freedom > > > > > > I ran again: > > > > > > reg <- lm(log(mean) ~ log(std.dev), data=eff.fro) > > > > > > and I get the pop-up: > > > The instruction at "0x6b4c45a5" referenced memory at "0x0032374a". > > > The memory could not be "read". Click OK to terminate > the program. > > > > > > > > > Any ideas? Thank you, > > > Adrian > > > > > > ______________________________________________ > > > R-help at stat.math.ethz.ch mailing list > > > https://www.stat.math.ethz.ch/mailman/listinfo/r-help > > > PLEASE do read the posting guide! > > > http://www.R-project.org/posting-guide.html > > > > > > > > > > > > > -------------------------------------------------------------- > ---------------- > > Notice: This e-mail message, together with any > attachments, contains > > information of Merck & Co., Inc. (One Merck Drive, > Whitehouse Station, New > > Jersey, USA 08889), and/or its affiliates (which may be > known outside the > > United States as Merck Frosst, Merck Sharp & Dohme or MSD > and in Japan as > > Banyu) that may be confidential, proprietary copyrighted > and/or legally > > privileged. It is intended solely for the use of the > individual or entity > > named on this message. 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