* using log directory 'd:/RCompile/CRANincoming/R-devel/rms.Rcheck' * using R Under development (unstable) (2024-12-02 r87417 ucrt) * using platform: x86_64-w64-mingw32 * R was compiled by gcc.exe (GCC) 13.3.0 GNU Fortran (GCC) 13.3.0 * running under: Windows Server 2022 x64 (build 20348) * using session charset: UTF-8 * checking for file 'rms/DESCRIPTION' ... OK * this is package 'rms' version '6.9-0' * checking CRAN incoming feasibility ... [12s] OK * checking package namespace information ... OK * checking package dependencies ... OK * checking if this is a source package ... OK * checking if there is a namespace ... OK * checking for hidden files and directories ... OK * checking for portable file names ... OK * checking whether package 'rms' can be installed ... OK * used C compiler: 'gcc.exe (GCC) 13.3.0' * used Fortran compiler: 'GNU Fortran (GCC) 13.3.0' * checking installed package size ... OK * checking package directory ... OK * checking for future file timestamps ... OK * checking DESCRIPTION meta-information ... OK * checking top-level files ... OK * checking for left-over files ... OK * checking index information ... OK * checking package subdirectories ... OK * checking code files for non-ASCII characters ... OK * checking R files for syntax errors ... OK * checking whether the package can be loaded ... OK * checking whether the package can be loaded with stated dependencies ... OK * checking whether the package can be unloaded cleanly ... OK * checking whether the namespace can be loaded with stated dependencies ... OK * checking whether the namespace can be unloaded cleanly ... OK * checking loading without being on the library search path ... OK * checking use of S3 registration ... OK * checking dependencies in R code ... OK * checking S3 generic/method consistency ... OK * checking replacement functions ... OK * checking foreign function calls ... OK * checking R code for possible problems ... [52s] OK * checking Rd files ... OK * checking Rd metadata ... OK * checking Rd line widths ... OK * checking Rd cross-references ... OK * checking for missing documentation entries ... OK * checking for code/documentation mismatches ... OK * checking Rd \usage sections ... OK * checking Rd contents ... OK * checking for unstated dependencies in examples ... OK * checking line endings in C/C++/Fortran sources/headers ... OK * checking pragmas in C/C++ headers and code ... OK * checking compilation flags used ... OK * checking compiled code ... OK * checking usage of KIND in Fortran files ... OK * checking examples ... [13s] ERROR Running examples in 'rms-Ex.R' failed The error most likely occurred in: > base::assign(".ptime", proc.time(), pos = "CheckExEnv") > ### Name: gIndex > ### Title: Calculate Total and Partial g-indexes for an rms Fit > ### Aliases: gIndex print.gIndex plot.gIndex > ### Keywords: predictive accuracy robust univar > > ### ** Examples > > set.seed(1) > n <- 40 > x <- 1:n > w <- factor(sample(c('a','b'), n, TRUE)) > u <- factor(sample(c('A','B'), n, TRUE)) > y <- .01*x + .2*(w=='b') + .3*(u=='B') + .2*(w=='b' & u=='B') + rnorm(n)/5 > dd <- datadist(x,w,u); options(datadist='dd') > f <- ols(y ~ x*w*u, x=TRUE, y=TRUE) > f Linear Regression Model ols(formula = y ~ x * w * u, x = TRUE, y = TRUE) Model Likelihood Discrimination Ratio Test Indexes Obs 40 LR chi2 42.69 R2 0.656 sigma0.1885 d.f. 7 R2 adj 0.581 d.f. 32 Pr(> chi2) 0.0000 g 0.263 Residuals Min 1Q Median 3Q Max -0.318329 -0.116336 0.001699 0.079795 0.472002 Coef S.E. t Pr(>|t|) Intercept 0.2011 0.1443 1.39 0.1732 x 0.0057 0.0057 0.99 0.3278 w=b 0.2414 0.2217 1.09 0.2843 u=B 0.1124 0.1719 0.65 0.5177 x * w=b -0.0034 0.0088 -0.38 0.7031 x * u=B 0.0043 0.0075 0.58 0.5662 w=b * u=B 0.0558 0.2717 0.21 0.8386 x * w=b * u=B 0.0051 0.0111 0.46 0.6480 > anova(f) Warning in anova.rms(f) : tests of nonlinear interaction with respect to single component variables ignore 3-way interactions Analysis of Variance Response: y Factor d.f. Partial SS MS F P x (Factor+Higher Order Factors) 4 0.4044281 0.1011070 2.85 0.0399 All Interactions 3 0.0583654 0.0194551 0.55 0.6533 w (Factor+Higher Order Factors) 4 0.7343790 0.1835948 5.17 0.0025 All Interactions 3 0.0642051 0.0214017 0.60 0.6182 u (Factor+Higher Order Factors) 4 0.7553646 0.1888412 5.32 0.0021 All Interactions 3 0.1240289 0.0413430 1.16 0.3388 x * w (Factor+Higher Order Factors) 2 0.0075815 0.0037907 0.11 0.8991 x * u (Factor+Higher Order Factors) 2 0.0582252 0.0291126 0.82 0.4497 w * u (Factor+Higher Order Factors) 2 0.0635351 0.0317676 0.89 0.4189 x * w * u (Factor+Higher Order Factors) 1 0.0075462 0.0075462 0.21 0.6480 TOTAL INTERACTION 4 0.1240951 0.0310238 0.87 0.4907 REGRESSION 7 2.1681606 0.3097372 8.72 <.0001 ERROR 32 1.1368328 0.0355260 > z <- list() > for(type in c('terms','cterms','ccterms')) + { + zc <- predict(f, type=type) + cat('type:', type, '\n') + print(zc) + z[[type]] <- zc + } type: terms x w u x * w x * u w * u x * w * u 1 -0.1105472 0.00000 0.00000 0.0000000 -0.0842429 0.000000 0.000000 2 -0.1048781 0.24144 0.00000 -0.0067938 -0.0799227 0.055783 0.010271 3 -0.0992090 0.00000 -0.11241 0.0000000 -0.0885630 0.000000 0.000000 4 -0.0935399 0.00000 0.00000 0.0000000 -0.0712825 0.000000 0.000000 5 -0.0878709 0.24144 0.00000 -0.0169845 -0.0669623 0.055783 0.025677 6 -0.0822018 0.00000 0.00000 0.0000000 -0.0626422 0.000000 0.000000 7 -0.0765327 0.00000 0.00000 0.0000000 -0.0583220 0.000000 0.000000 8 -0.0708636 0.00000 0.00000 0.0000000 -0.0540019 0.000000 0.000000 9 -0.0651945 0.24144 -0.11241 -0.0305720 -0.0885630 0.000000 0.000000 10 -0.0595254 0.24144 -0.11241 -0.0339689 -0.0885630 0.000000 0.000000 11 -0.0538563 0.00000 0.00000 0.0000000 -0.0410414 0.000000 0.000000 12 -0.0481872 0.00000 -0.11241 0.0000000 -0.0885630 0.000000 0.000000 13 -0.0425182 0.00000 0.00000 0.0000000 -0.0324011 0.000000 0.000000 14 -0.0368491 0.00000 0.00000 0.0000000 -0.0280810 0.000000 0.000000 15 -0.0311800 0.00000 -0.11241 0.0000000 -0.0885630 0.000000 0.000000 16 -0.0255109 0.24144 -0.11241 -0.0543502 -0.0885630 0.000000 0.000000 17 -0.0198418 0.24144 0.00000 -0.0577471 -0.0151205 0.055783 0.087302 18 -0.0141727 0.24144 0.00000 -0.0611440 -0.0108004 0.055783 0.092437 19 -0.0085036 0.24144 0.00000 -0.0645409 -0.0064802 0.055783 0.097573 20 -0.0028345 0.00000 -0.11241 0.0000000 -0.0885630 0.000000 0.000000 21 0.0028345 0.00000 -0.11241 0.0000000 -0.0885630 0.000000 0.000000 22 0.0085036 0.00000 0.00000 0.0000000 0.0064802 0.000000 0.000000 23 0.0141727 0.00000 0.00000 0.0000000 0.0108004 0.000000 0.000000 24 0.0198418 0.00000 0.00000 0.0000000 0.0151205 0.000000 0.000000 25 0.0255109 0.00000 0.00000 0.0000000 0.0194407 0.000000 0.000000 26 0.0311800 0.00000 0.00000 0.0000000 0.0237608 0.000000 0.000000 27 0.0368491 0.24144 0.00000 -0.0917160 0.0280810 0.055783 0.138656 28 0.0425182 0.00000 -0.11241 0.0000000 -0.0885630 0.000000 0.000000 29 0.0481872 0.00000 0.00000 0.0000000 0.0367213 0.000000 0.000000 30 0.0538563 0.24144 0.00000 -0.1019067 0.0410414 0.055783 0.154062 31 0.0595254 0.24144 0.00000 -0.1053036 0.0453616 0.055783 0.159197 32 0.0651945 0.24144 0.00000 -0.1087005 0.0496817 0.055783 0.164333 33 0.0708636 0.00000 -0.11241 0.0000000 -0.0885630 0.000000 0.000000 34 0.0765327 0.24144 -0.11241 -0.1154943 -0.0885630 0.000000 0.000000 35 0.0822018 0.00000 -0.11241 0.0000000 -0.0885630 0.000000 0.000000 36 0.0878709 0.00000 0.00000 0.0000000 0.0669623 0.000000 0.000000 37 0.0935399 0.24144 0.00000 -0.1256849 0.0712825 0.055783 0.190010 38 0.0992090 0.00000 -0.11241 0.0000000 -0.0885630 0.000000 0.000000 39 0.1048781 0.24144 -0.11241 -0.1324787 -0.0885630 0.000000 0.000000 40 0.1105472 0.24144 0.00000 -0.1358756 0.0842429 0.055783 0.205416 type: cterms x w u 1 0.0099892 0.00000 0.11673 2 0.0234555 0.30070 0.18710 3 0.0170073 0.00000 0.00000 4 0.0399569 0.00000 0.12969 5 0.0586387 0.30592 0.21547 6 0.0599354 0.00000 0.13833 7 0.0699247 0.00000 0.14265 8 0.0799139 0.00000 0.14697 9 0.0204498 0.21087 0.00000 10 0.0227220 0.20747 0.00000 11 0.1098816 0.00000 0.15993 12 0.0680290 0.00000 0.00000 13 0.1298601 0.00000 0.16857 14 0.1398493 0.00000 0.17289 15 0.0850363 0.00000 0.00000 16 0.0363552 0.18709 0.00000 17 0.1993717 0.32678 0.32894 18 0.2110994 0.32852 0.33839 19 0.2228272 0.33026 0.34785 20 0.1133817 0.00000 0.00000 21 0.1190508 0.00000 0.00000 22 0.2197632 0.00000 0.20745 23 0.2297524 0.00000 0.21177 24 0.2397417 0.00000 0.21609 25 0.2497309 0.00000 0.22041 26 0.2597201 0.00000 0.22473 27 0.3166491 0.34416 0.42349 28 0.1587344 0.00000 0.00000 29 0.2896878 0.00000 0.23769 30 0.3518324 0.34938 0.45186 31 0.3635601 0.35112 0.46131 32 0.3752879 0.35286 0.47077 33 0.1870799 0.00000 0.00000 34 0.0772547 0.12595 0.00000 35 0.1984181 0.00000 0.00000 36 0.3596125 0.00000 0.26793 37 0.4339266 0.36155 0.51805 38 0.2154253 0.00000 0.00000 39 0.0886157 0.10896 0.00000 40 0.4691098 0.36677 0.54641 type: ccterms x, u, w [1,] 0.122398 [2,] 0.433089 [3,] 0.017007 [4,] 0.152365 [5,] 0.468272 [6,] 0.172344 [7,] 0.182333 [8,] 0.192322 [9,] 0.261892 [10,] 0.264164 [11,] 0.222290 [12,] 0.068029 [13,] 0.242269 [14,] 0.252258 [15,] 0.085036 [16,] 0.277797 [17,] 0.609005 [18,] 0.620733 [19,] 0.632461 [20,] 0.113382 [21,] 0.119051 [22,] 0.332172 [23,] 0.342161 [24,] 0.352150 [25,] 0.362139 [26,] 0.372129 [27,] 0.726283 [28,] 0.158734 [29,] 0.402096 [30,] 0.761466 [31,] 0.773194 [32,] 0.784921 [33,] 0.187080 [34,] 0.318697 [35,] 0.198418 [36,] 0.472021 [37,] 0.843560 [38,] 0.215425 [39,] 0.330058 [40,] 0.878743 > > zc <- z$cterms > GiniMd(zc[, 1]) [1] 0.14287 > GiniMd(zc[, 2]) [1] 0.15475 > GiniMd(zc[, 3]) [1] 0.18792 > GiniMd(f$linear.predictors) [1] 0.26271 > g <- gIndex(f) > g g Index: y ~ x * w * u y x, u, w 0.2627 Total 0.2627 > g['Total',] [1] 0.26271 > gIndex(f, partials=FALSE) g Index: y ~ x * w * u y Total 0.2627 > gIndex(f, type='cterms') g Index: y ~ x * w * u y x 0.1429 w 0.1548 u 0.1879 Total 0.2627 > gIndex(f, type='terms') g Index: y ~ x * w * u y x 0.07748 w 0.11886 u 0.05246 x * w 0.04593 x * u 0.06386 w * u 0.02281 x * w * u 0.05453 Total 0.26271 > > y <- y > .8 > f <- lrm(y ~ x * w * u, x=TRUE, y=TRUE, opt_method='BFGS') Error in solve.default(info, tol = tol) : system is computationally singular: reciprocal condition number = 5.50905e-20 Error in solve.default(info, tol = tol) : system is computationally singular: reciprocal condition number = 5.50905e-20 Warning in lrm(y ~ x * w * u, x = TRUE, y = TRUE, opt_method = "BFGS") : Unable to fit model using "lrm.fit" > # or f <- lrm(y ~ x * w * u, x=TRUE, y=TRUE, reltol=1e-6) > > gIndex(f, fun=plogis, funlabel='Prob[y=1]') Warning in structure(limits, class = "data.frame", row.names = c("Low:effect", : Calling 'structure(NULL, *)' is deprecated, as NULL cannot have attributes. Consider 'structure(list(), *)' instead. Error in formula.character(object, env = baseenv()) : invalid formula "NULL": not a call Calls: gIndex ... removeFormulaTerms -> as.formula -> formula -> formula.character Execution halted * checking PDF version of manual ... [21s] OK * checking HTML version of manual ... [22s] OK * DONE Status: 1 ERROR