Last updated on 2019-07-03 01:47:31 CEST.
| Flavor | Version | Tinstall | Tcheck | Ttotal | Status | Flags |
|---|---|---|---|---|---|---|
| r-devel-linux-x86_64-debian-clang | 3.1-140 | 26.73 | 228.27 | 255.00 | OK | |
| r-devel-linux-x86_64-debian-gcc | 3.1-140 | 21.11 | 172.37 | 193.48 | OK | |
| r-devel-linux-x86_64-fedora-clang | 3.1-140 | 304.79 | OK | |||
| r-devel-linux-x86_64-fedora-gcc | 3.1-140 | 290.60 | OK | |||
| r-devel-windows-ix86+x86_64 | 3.1-140 | 51.00 | 493.00 | 544.00 | OK | |
| r-patched-linux-x86_64 | 3.1-140 | 24.99 | 227.11 | 252.10 | OK | |
| r-patched-solaris-x86 | 3.1-140 | OK | ||||
| r-release-linux-x86_64 | 3.1-140 | 26.23 | 226.55 | 252.78 | OK | |
| r-release-windows-ix86+x86_64 | 3.1-140 | 56.00 | 482.00 | 538.00 | OK | |
| r-release-osx-x86_64 | 3.1-140 | OK | ||||
| r-oldrel-windows-ix86+x86_64 | 3.1-140 | 45.00 | 341.00 | 386.00 | ERROR | |
| r-oldrel-osx-x86_64 | 3.1-140 | OK |
Version: 3.1-140
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: 3.1-140
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: 3.1-140
Check: running tests for arch ‘i386’
Result: ERROR
Running 'anova.gls.R' [1s]
Running 'augPred_lab.R' [26s]
Running 'augPredmissing.R' [1s]
Running 'coef.R' [1s]
Comparing 'coef.Rout' to 'coef.Rout.save' ... OK
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 'lme.R' [5s]
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' [2s]
Running 'nlme2.R' [2s]
Running 'predict.lme.R' [1s]
Running 'sigma-fixed-etc.R' [20s]
Running 'updateLme.R' [1s]
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; 2019-03-11 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: 3.1-140
Check: running tests for arch ‘x64’
Result: ERROR
Running 'anova.gls.R' [1s]
Running 'augPred_lab.R' [25s]
Running 'augPredmissing.R' [0s]
Running 'coef.R' [0s]
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' [0s]
Running 'getData.R' [1s]
Running 'gls.R' [0s]
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' [19s]
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
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