CRAN Package Check Results for Package nlme

Last updated on 2019-09-23 09:50:52 CEST.

Flavor Version Tinstall Tcheck Ttotal Status Flags
r-devel-linux-x86_64-debian-clang 3.1-141 27.78 225.79 253.57 OK
r-devel-linux-x86_64-debian-gcc 3.1-141 22.40 167.64 190.04 OK
r-devel-linux-x86_64-fedora-clang 3.1-141 296.20 OK
r-devel-linux-x86_64-fedora-gcc 3.1-141 294.43 OK
r-devel-windows-ix86+x86_64 3.1-141 74.00 487.00 561.00 OK
r-patched-linux-x86_64 3.1-141 24.29 222.50 246.79 OK
r-patched-solaris-x86 3.1-141 OK
r-release-linux-x86_64 3.1-141 24.92 222.06 246.98 OK
r-release-windows-ix86+x86_64 3.1-141 79.00 472.00 551.00 OK
r-release-osx-x86_64 3.1-141 OK
r-oldrel-windows-ix86+x86_64 3.1-141 47.00 325.00 372.00 ERROR
r-oldrel-osx-x86_64 3.1-141 OK

Check Details

Version: 3.1-141
Check: running examples for arch ‘i386’
Result: 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
Flavor: r-oldrel-windows-ix86+x86_64

Version: 3.1-141
Check: running examples for arch ‘x64’
Result: 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
Flavor: r-oldrel-windows-ix86+x86_64

Version: 3.1-141
Check: running tests for arch ‘i386’
Result: ERROR
     Running 'anova.gls.R' [1s]
     Running 'augPred_lab.R' [25s]
     Running 'augPredmissing.R' [1s]
     Running 'coef.R' [0s]
     Comparing 'coef.Rout' to 'coef.Rout.save' ... OK
     Running 'contrMat.R' [1s]
     Running 'data.frame.R' [0s]
     Running 'deparse.R' [1s]
     Running 'deviance.R' [1s]
     Running 'fitted.R' [0s]
     Running 'getData.R' [1s]
     Running 'gls.R' [0s]
     Running 'gnls-ch8.R' [1s]
     Running 'lmList.R' [1s]
     Running 'lme.R' [4s]
     Comparing 'lme.Rout' to 'lme.Rout.save' ...92,95c92
    < Error in logLik.lmeStructInt(lmeSt, lmePars) :
    < 'Calloc' could not allocate memory (890472804 of 8 bytes)
    < In addition: Warning message:
    < In lme.formula(distance ~ 1, data = Orthodont, random = ~Subject) :
    ---
    > Error in lme.formula(distance ~ 1, data = Orthodont, random = ~Subject) :
     Running 'missing.R' [1s]
     Comparing 'missing.Rout' to 'missing.Rout.save' ... OK
     Running 'nlme-stall.R' [0s]
     Running 'nlme.R' [1s]
     Running 'nlme2.R' [2s]
     Running 'predict.lme.R' [1s]
     Running 'sigma-fixed-etc.R' [18s]
     Running 'updateLme.R' [2s]
     Running 'varIdent.R' [0s]
    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 <R-core@R-project.org>
     Repository: CRAN
     Date/Publication: 2018-04-07 12:20:09 UTC
     Built: R 3.5.3; x86_64-w64-mingw32; 2019-03-11 11:00:56 UTC; windows
    
     -- File: D:/RCompile/recent/R-3.5.3/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 -> <Anonymous>
     Execution halted
Flavor: r-oldrel-windows-ix86+x86_64

Version: 3.1-141
Check: running tests for arch ‘x64’
Result: ERROR
     Running 'anova.gls.R' [1s]
     Running 'augPred_lab.R' [24s]
     Running 'augPredmissing.R' [1s]
     Running 'coef.R' [1s]
     Comparing 'coef.Rout' to 'coef.Rout.save' ... OK
     Running 'contrMat.R' [1s]
     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 'lme.R' [10s]
     Running 'missing.R' [1s]
     Comparing 'missing.Rout' to 'missing.Rout.save' ... OK
     Running 'nlme-stall.R' [0s]
     Running 'nlme.R' [2s]
     Running 'nlme2.R' [2s]
     Running 'predict.lme.R' [1s]
     Running 'sigma-fixed-etc.R' [18s]
     Running 'updateLme.R' [1s]
     Running 'varIdent.R' [0s]
    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 <R-core@R-project.org>
     Repository: CRAN
     Date/Publication: 2018-04-07 12:20:09 UTC
     Built: R 3.5.3; x86_64-w64-mingw32; 2019-03-11 11:00:56 UTC; windows
    
     -- File: D:/RCompile/recent/R-3.5.3/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 -> <Anonymous>
     Execution halted
    Running the tests in 'tests/lme.R' failed.
    Complete output:
     > library(nlme)
     >
     > options(digits = 6)# <==> less platform dependency in print() output
     > if(!dev.interactive(orNone=TRUE)) pdf("test_lme.pdf")
     >
     > fm1 <- lmList(Oxboys)
     > fm1
     Call:
     Model: height ~ age | Subject
     Data: Oxboys
    
     Coefficients:
     (Intercept) age
     10 130.262 3.72291
     26 137.993 5.58878
     25 139.210 4.02408
     9 138.137 6.00906
     2 142.858 5.44018
     6 146.791 3.96317
     7 146.128 4.99005
     17 142.978 8.61178
     16 147.545 4.54520
     15 144.276 7.12426
     8 148.293 6.46471
     20 151.471 4.37447
     1 148.120 7.17815
     18 151.180 5.95779
     5 151.429 6.24613
     23 151.065 7.18512
     11 150.047 8.50608
     21 150.521 7.49779
     3 155.651 4.77467
     24 153.140 6.76470
     22 154.567 8.08751
     12 156.811 7.01547
     13 156.071 8.49381
     14 159.474 8.67089
     19 164.576 9.06562
     4 165.072 9.36056
    
     Degrees of freedom: 234 total; 182 residual
     Residual standard error: 0.659888
     > fm2 <- lme(fm1)
     > fm2
     Linear mixed-effects model fit by REML
     Data: Oxboys
     Log-restricted-likelihood: -362.045
     Fixed: height ~ age
     (Intercept) age
     149.37175 6.52547
    
     Random effects:
     Formula: ~age | Subject
     Structure: General positive-definite, Log-Cholesky parametrization
     StdDev Corr
     (Intercept) 8.081077 (Intr)
     age 1.680717 0.641
     Residual 0.659889
    
     Number of Observations: 234
     Number of Groups: 26
     > vc2 <- VarCorr(fm2)
     > stopifnot(
     + all.equal(fixef(fm2), c("(Intercept)" = 149.371753,
     + age = 6.52546866), tol=1e-8),
     + all.equal(as.numeric(vc2[,"StdDev"]),
     + c(8.081077, 1.680717, 0.659889), tol=4e-7))
     >
     > # bug report from Arne.Mueller@sanofi-aventis.com
     > mod <- distance ~ age + Sex
     > fm3 <- lme(mod, Orthodont, random = ~ 1)
     > pm3 <- predict(fm3, Orthodont)
     > stopifnot(all.equal(mean(pm3), 24.023148148),
     + all.equal( sd(pm3), 2.4802195115),
     + all.equal(quantile(pm3), c("0%" = 17.0817792, "25%" = 22.3481813,
     + "50%" = 23.9271016, "75%" = 25.5740014,
     + "100%"= 30.8662241)))
     >
     >
     > ## bug report and fix from Dimitris Rizopoulos and Spencer Graves:
     > ## when 'returnObject = TRUE', do not stop() but give warning() on non-convergence:
     > tools::assertWarning(
     + fm1 <- lme(distance ~ age, data = Orthodont,
     + control = lmeControl(msMaxIter = 1, returnObject = TRUE))
     + )
     >
     > ## "typo" in 'random=' -- giving 27-dim. vector random effect:
     > ## PR#17524 B.Tyner: https://bugs.r-project.org/bugzilla/show_bug.cgi?id=17524
     > try(lme(distance ~ 1, data=Orthodont, random = ~ Subject))
Flavor: r-oldrel-windows-ix86+x86_64