* using log directory 'd:/Rcompile/CRANpkg/local/3.4/nlme.Rcheck' * using R version 3.4.4 (2018-03-15) * using platform: x86_64-w64-mingw32 (64-bit) * using session charset: ISO8859-1 * checking for file 'nlme/DESCRIPTION' ... OK * this is package 'nlme' version '3.1-139' * package encoding: UTF-8 * 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 'nlme' can be installed ... OK * checking installed package size ... OK * checking package directory ... 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 R files for non-ASCII characters ... OK * checking R files for syntax errors ... OK * loading checks for arch 'i386' ** 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 use of S3 registration ... OK * loading checks for arch 'x64' ** 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 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 ... [49s] NOTE lme.formula: no visible global function definition for 'isFALSE' Undefined global functions or variables: isFALSE * checking Rd files ... OK * checking Rd metadata ... 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 contents of 'data' directory ... OK * checking data for non-ASCII characters ... OK * checking data for ASCII and uncompressed saves ... OK * checking line endings in C/C++/Fortran sources/headers ... OK * checking line endings in Makefiles ... OK * checking compilation flags in Makevars ... OK * checking for GNU extensions in Makefiles ... OK * checking for portable use of $(BLAS_LIBS) and $(LAPACK_LIBS) ... OK * checking compiled code ... OK * checking examples ... ** running examples for arch 'i386' ... ERROR Running examples in 'nlme-Ex.R' failed The error most likely occurred in: > ### Name: pairs.compareFits > ### Title: Pairs Plot of compareFits Object > ### Aliases: pairs.compareFits > ### Keywords: models > > ### ** Examples > > example(compareFits) # cF12 <- compareFits(coef(lmList(Orthodont)), .. lme(*)) cmprFt> fm1 <- lmList(Orthodont) cmprFt> fm2 <- lme(fm1) cmprFt> compareFits(coef(fm1), coef(fm2)) , , (Intercept) coef(fm1) coef(fm2) M16 16.95 16.57335 M05 13.65 15.58444 M02 14.85 16.03361 M11 20.05 17.65160 M07 14.95 16.15314 M08 19.75 17.62141 M03 16.00 16.58721 M12 13.25 15.76312 M13 2.80 12.63156 M14 19.10 17.66546 M09 14.40 16.31671 M15 13.50 16.22614 M06 18.95 17.97875 M04 24.70 19.76157 M01 17.30 17.81269 M10 21.25 19.41435 F10 13.55 14.47973 F09 18.10 16.47016 F06 17.00 16.14053 F01 17.25 16.27515 F05 19.60 17.27792 F07 16.95 16.57335 F02 14.20 15.74926 F08 21.45 18.01143 F03 14.40 15.98832 F04 19.65 17.83027 F11 18.95 17.97875 , , age coef(fm1) coef(fm2) M16 0.550 0.5913314 M05 0.850 0.6857856 M02 0.775 0.6746930 M11 0.325 0.5413592 M07 0.800 0.6950852 M08 0.375 0.5654489 M03 0.750 0.6960376 M12 1.000 0.7747494 M13 1.950 1.0738542 M14 0.525 0.6460653 M09 0.975 0.7960939 M15 1.125 0.8683630 M06 0.675 0.7433764 M04 0.175 0.5943002 M01 0.950 0.8758698 M10 0.750 0.8713317 F10 0.450 0.4095946 F09 0.275 0.4421434 F06 0.375 0.4736281 F01 0.375 0.4819754 F05 0.275 0.4922274 F07 0.550 0.5913314 F02 0.800 0.6700432 F08 0.175 0.4857848 F03 0.850 0.7108276 F04 0.475 0.6303230 F11 0.675 0.7433764 > plot(cF12) Error in plot(cF12) : object 'cF12' not found Execution halted ** running examples for arch 'x64' ... ERROR Running examples in 'nlme-Ex.R' failed The error most likely occurred in: > ### Name: pairs.compareFits > ### Title: Pairs Plot of compareFits Object > ### Aliases: pairs.compareFits > ### Keywords: models > > ### ** Examples > > example(compareFits) # cF12 <- compareFits(coef(lmList(Orthodont)), .. lme(*)) cmprFt> fm1 <- lmList(Orthodont) cmprFt> fm2 <- lme(fm1) cmprFt> compareFits(coef(fm1), coef(fm2)) , , (Intercept) coef(fm1) coef(fm2) M16 16.95 16.57335 M05 13.65 15.58444 M02 14.85 16.03361 M11 20.05 17.65160 M07 14.95 16.15314 M08 19.75 17.62141 M03 16.00 16.58721 M12 13.25 15.76312 M13 2.80 12.63156 M14 19.10 17.66546 M09 14.40 16.31671 M15 13.50 16.22614 M06 18.95 17.97875 M04 24.70 19.76157 M01 17.30 17.81269 M10 21.25 19.41435 F10 13.55 14.47973 F09 18.10 16.47016 F06 17.00 16.14053 F01 17.25 16.27515 F05 19.60 17.27792 F07 16.95 16.57335 F02 14.20 15.74926 F08 21.45 18.01143 F03 14.40 15.98832 F04 19.65 17.83027 F11 18.95 17.97875 , , age coef(fm1) coef(fm2) M16 0.550 0.5913314 M05 0.850 0.6857856 M02 0.775 0.6746930 M11 0.325 0.5413592 M07 0.800 0.6950852 M08 0.375 0.5654489 M03 0.750 0.6960376 M12 1.000 0.7747493 M13 1.950 1.0738541 M14 0.525 0.6460653 M09 0.975 0.7960939 M15 1.125 0.8683629 M06 0.675 0.7433764 M04 0.175 0.5943002 M01 0.950 0.8758698 M10 0.750 0.8713317 F10 0.450 0.4095946 F09 0.275 0.4421434 F06 0.375 0.4736281 F01 0.375 0.4819755 F05 0.275 0.4922275 F07 0.550 0.5913314 F02 0.800 0.6700432 F08 0.175 0.4857848 F03 0.850 0.7108276 F04 0.475 0.6303230 F11 0.675 0.7433764 > plot(cF12) Error in plot(cF12) : object 'cF12' not found Execution halted * checking for unstated dependencies in 'tests' ... OK * checking tests ... ** running tests for arch 'i386' ... [31s] ERROR Running 'anova.gls.R' [1s] Running 'augPred_lab.R' [21s] Running 'augPredmissing.R' [1s] Running 'coef.R' [0s] Comparing 'coef.Rout' to 'coef.Rout.save' ...13,23c13,24 < Classes 'varIdent', 'varFunc' atomic [1:2] 0.0953 0.131 < ..- attr(*, "groupNames")= chr [1:4] "8" "10" "14" "12" < ..- attr(*, "fixed")= Named num 0.113 < .. ..- attr(*, "names")= chr "12" < ..- attr(*, "formula")=Class 'formula' language ~1 | age < .. .. ..- attr(*, ".Environment")= < ..- attr(*, "groups")= chr [1:108] "8" "10" "12" "14" ... < ..- attr(*, "whichFix")= logi [1:3] FALSE FALSE TRUE < ..- attr(*, "weights")= Named num [1:108] 1 0.909 0.893 0.877 1 ... < .. ..- attr(*, "names")= chr [1:108] "8" "10" "12" "14" ... < ..- attr(*, "logLik")= num -9.17 --- > 'varIdent' Named num [1:2] 0.0953 0.131 > - attr(*, "names")= chr [1:2] "10" "14" > - attr(*, "groupNames")= chr [1:4] "8" "10" "14" "12" > - attr(*, "fixed")= Named num 0.113 > ..- attr(*, "names")= chr "12" > - attr(*, "formula")=Class 'formula' language ~1 | age > .. ..- attr(*, ".Environment")= > - attr(*, "groups")= chr [1:108] "8" "10" "12" "14" ... > - attr(*, "whichFix")= logi [1:3] FALSE FALSE TRUE > - attr(*, "weights")= Named num [1:108] 1 0.909 0.893 0.877 1 ... > ..- attr(*, "names")= chr [1:108] "8" "10" "12" "14" ... > - attr(*, "logLik")= num -9.17 Running 'contrMat.R' [0s] Running 'data.frame.R' [0s] Running 'deparse.R' [1s] Running 'deviance.R' [1s] Running 'fitted.R' [1s] Running 'getData.R' [1s] Running 'gls.R' [0s] Running 'gnls-ch8.R' [1s] Running 'lmList.R' [1s] Running the tests in 'tests/lmList.R' failed. Complete output: > ## PR#13788 > > library(nlme) > packageDescription("nlme")# gets the .Library one even in R CMD checking < FIXME ! Package: nlme Version: 3.1-137 Date: 2018-04-07 Priority: recommended Title: Linear and Nonlinear Mixed Effects Models Authors@R: c(person("José", "Pinheiro", role = "aut", comment = "S version"), person("Douglas", "Bates", role = "aut", comment = "up to 2007"), person("Saikat", "DebRoy", role = "ctb", comment = "up to 2002"), person("Deepayan", "Sarkar", role = "ctb", comment = "up to 2005"), person("EISPACK authors", role = "ctb", comment = "src/rs.f"), person("Siem", "Heisterkamp", role = "ctb", comment = "Author fixed sigma"), person("Bert", "Van Willigen",role = "ctb", comment = "Programmer fixed sigma"), person("R-core", email = "R-core@R-project.org", role = c("aut", "cre"))) Description: Fit and compare Gaussian linear and nonlinear mixed-effects models. Depends: R (>= 3.4.0) Imports: graphics, stats, utils, lattice Suggests: Hmisc, MASS LazyData: yes ByteCompile: yes Encoding: UTF-8 License: GPL (>= 2) | file LICENCE BugReports: https://bugs.r-project.org NeedsCompilation: yes Packaged: 2018-04-07 08:11:41 UTC; ripley Author: José Pinheiro [aut] (S version), Douglas Bates [aut] (up to 2007), Saikat DebRoy [ctb] (up to 2002), Deepayan Sarkar [ctb] (up to 2005), EISPACK authors [ctb] (src/rs.f), Siem Heisterkamp [ctb] (Author fixed sigma), Bert Van Willigen [ctb] (Programmer fixed sigma), R-core [aut, cre] Maintainer: R-core Repository: CRAN Date/Publication: 2018-04-07 12:20:47 UTC Built: R 3.4.4; x86_64-w64-mingw32; 2018-09-03 14:15:00 UTC; windows -- File: D:/RCompile/recent/R-3.4.4/library/nlme/Meta/package.rds > > qm <- lmList(height ~ age | Subject, data = Oxboys) > nd <- with(Oxboys, + expand.grid(age = seq(min(age),max(age),length=50), + Subject = levels(Subject)) + ) > > ## failed in 3.1-92 > res <- predict(qm, nd, se=TRUE) > stopifnot(is.data.frame(res), dim(res) == c(1300, 3), + identical(names(res), c("Subject", "fit", "se.fit"))) > > req <- ranef(qm) > (p.req <- plot(req, xlab = "R.Eff.", ylab = "Subj")) > # Fails (p.re2 <- plot(req, age ~ fitted(.))) > iqm <- intervals(qm) > stopifnot(is.array(iqm), dim(iqm) == c(26,3,2)) > p.iq <- plot(iqm, ylab = "Subject [factor]") Error in bwplot.formula(x = group ~ intervals | what, data = list(group = c(1L, : formal argument "ylab" matched by multiple actual arguments Calls: plot ... dotplot.formula -> eval.parent -> eval -> eval -> Execution halted ** running tests for arch 'x64' ... [32s] ERROR Running 'anova.gls.R' [1s] Running 'augPred_lab.R' [23s] Running 'augPredmissing.R' [1s] Running 'coef.R' [0s] Comparing 'coef.Rout' to 'coef.Rout.save' ...13,23c13,24 < Classes 'varIdent', 'varFunc' atomic [1:2] 0.0953 0.131 < ..- attr(*, "groupNames")= chr [1:4] "8" "10" "14" "12" < ..- attr(*, "fixed")= Named num 0.113 < .. ..- attr(*, "names")= chr "12" < ..- attr(*, "formula")=Class 'formula' language ~1 | age < .. .. ..- attr(*, ".Environment")= < ..- attr(*, "groups")= chr [1:108] "8" "10" "12" "14" ... < ..- attr(*, "whichFix")= logi [1:3] FALSE FALSE TRUE < ..- attr(*, "weights")= Named num [1:108] 1 0.909 0.893 0.877 1 ... < .. ..- attr(*, "names")= chr [1:108] "8" "10" "12" "14" ... < ..- attr(*, "logLik")= num -9.17 --- > 'varIdent' Named num [1:2] 0.0953 0.131 > - attr(*, "names")= chr [1:2] "10" "14" > - attr(*, "groupNames")= chr [1:4] "8" "10" "14" "12" > - attr(*, "fixed")= Named num 0.113 > ..- attr(*, "names")= chr "12" > - attr(*, "formula")=Class 'formula' language ~1 | age > .. ..- attr(*, ".Environment")= > - attr(*, "groups")= chr [1:108] "8" "10" "12" "14" ... > - attr(*, "whichFix")= logi [1:3] FALSE FALSE TRUE > - attr(*, "weights")= Named num [1:108] 1 0.909 0.893 0.877 1 ... > ..- attr(*, "names")= chr [1:108] "8" "10" "12" "14" ... > - attr(*, "logLik")= num -9.17 Running 'contrMat.R' [0s] Running 'data.frame.R' [0s] Running 'deparse.R' [1s] Running 'deviance.R' [1s] Running 'fitted.R' [0s] Running 'getData.R' [1s] Running 'gls.R' [1s] Running 'gnls-ch8.R' [1s] Running 'lmList.R' [1s] Running the tests in 'tests/lmList.R' failed. Complete output: > ## PR#13788 > > library(nlme) > packageDescription("nlme")# gets the .Library one even in R CMD checking < FIXME ! Package: nlme Version: 3.1-137 Date: 2018-04-07 Priority: recommended Title: Linear and Nonlinear Mixed Effects Models Authors@R: c(person("José", "Pinheiro", role = "aut", comment = "S version"), person("Douglas", "Bates", role = "aut", comment = "up to 2007"), person("Saikat", "DebRoy", role = "ctb", comment = "up to 2002"), person("Deepayan", "Sarkar", role = "ctb", comment = "up to 2005"), person("EISPACK authors", role = "ctb", comment = "src/rs.f"), person("Siem", "Heisterkamp", role = "ctb", comment = "Author fixed sigma"), person("Bert", "Van Willigen",role = "ctb", comment = "Programmer fixed sigma"), person("R-core", email = "R-core@R-project.org", role = c("aut", "cre"))) Description: Fit and compare Gaussian linear and nonlinear mixed-effects models. Depends: R (>= 3.4.0) Imports: graphics, stats, utils, lattice Suggests: Hmisc, MASS LazyData: yes ByteCompile: yes Encoding: UTF-8 License: GPL (>= 2) | file LICENCE BugReports: https://bugs.r-project.org NeedsCompilation: yes Packaged: 2018-04-07 08:11:41 UTC; ripley Author: José Pinheiro [aut] (S version), Douglas Bates [aut] (up to 2007), Saikat DebRoy [ctb] (up to 2002), Deepayan Sarkar [ctb] (up to 2005), EISPACK authors [ctb] (src/rs.f), Siem Heisterkamp [ctb] (Author fixed sigma), Bert Van Willigen [ctb] (Programmer fixed sigma), R-core [aut, cre] Maintainer: R-core Repository: CRAN Date/Publication: 2018-04-07 12:20:47 UTC Built: R 3.4.4; x86_64-w64-mingw32; 2018-09-03 14:15:00 UTC; windows -- File: D:/RCompile/recent/R-3.4.4/library/nlme/Meta/package.rds > > qm <- lmList(height ~ age | Subject, data = Oxboys) > nd <- with(Oxboys, + expand.grid(age = seq(min(age),max(age),length=50), + Subject = levels(Subject)) + ) > > ## failed in 3.1-92 > res <- predict(qm, nd, se=TRUE) > stopifnot(is.data.frame(res), dim(res) == c(1300, 3), + identical(names(res), c("Subject", "fit", "se.fit"))) > > req <- ranef(qm) > (p.req <- plot(req, xlab = "R.Eff.", ylab = "Subj")) > # Fails (p.re2 <- plot(req, age ~ fitted(.))) > iqm <- intervals(qm) > stopifnot(is.array(iqm), dim(iqm) == c(26,3,2)) > p.iq <- plot(iqm, ylab = "Subject [factor]") Error in bwplot.formula(x = group ~ intervals | what, data = list(group = c(1L, : formal argument "ylab" matched by multiple actual arguments Calls: plot ... dotplot.formula -> eval.parent -> eval -> eval -> Execution halted * checking PDF version of manual ... OK * DONE Status: 4 ERRORs, 1 NOTE