Running 'anova.gls.R' [2s]
  Running 'augPred_lab.R' [29s]
  Running 'augPredmissing.R' [1s]
  Running 'coef.R' [1s]
  Comparing 'coef.Rout' to 'coef.Rout.save' ... OK
  Running 'contrMat.R' [1s]
  Running 'data.frame.R' [1s]
  Running 'deparse.R' [1s]
  Running 'deviance.R' [1s]
  Running 'fitted.R' [1s]
  Running 'getData.R' [1s]
  Running 'gls.R' [1s]
  Running 'gnls-ch8.R' [2s]
  Running 'lmList.R' [1s]
  Running 'lme.R' [11s]
  Running 'missing.R' [1s]
  Comparing 'missing.Rout' to 'missing.Rout.save' ... OK
  Running 'nlme-stall.R' [0s]
  Running 'nlme.R' [3s]
  Running 'nlme2.R' [2s]
  Running 'predict.lme.R' [1s]
  Running 'sigma-fixed-etc.R' [22s]
  Running 'updateLme.R' [2s]
  Running 'varIdent.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 <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; 2019-04-04 15:11:55 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))