CRAN Package Check Results for Package lme4

Last updated on 2022-01-24 23:54:31 CET.

Flavor Version Tinstall Tcheck Ttotal Status Flags
r-devel-linux-x86_64-debian-clang 1.1-27.1 108.53 561.24 669.77 OK
r-devel-linux-x86_64-debian-gcc 1.1-27.1 78.34 419.05 497.39 OK
r-devel-linux-x86_64-fedora-clang 1.1-27.1 837.56 ERROR
r-devel-linux-x86_64-fedora-gcc 1.1-27.1 837.55 ERROR
r-devel-windows-x86_64-new-UL 1.1-27.1 236.00 536.00 772.00 NOTE
r-devel-windows-x86_64-new-TK 1.1-27.1 ERROR
r-patched-linux-x86_64 1.1-27.1 97.20 524.00 621.20 OK
r-release-linux-x86_64 1.1-27.1 89.80 518.41 608.21 OK
r-release-macos-arm64 1.1-27.1 NOTE
r-release-macos-x86_64 1.1-27.1 NOTE
r-release-windows-ix86+x86_64 1.1-27.1 230.00 702.00 932.00 NOTE
r-oldrel-macos-x86_64 1.1-27.1 NOTE
r-oldrel-windows-ix86+x86_64 1.1-27.1 224.00 693.00 917.00 NOTE

Check Details

Version: 1.1-27.1
Check: installed package size
Result: NOTE
     installed size is 24.9Mb
     sub-directories of 1Mb or more:
     R 1.5Mb
     doc 2.0Mb
     libs 19.3Mb
     testdata 1.3Mb
Flavors: r-devel-linux-x86_64-fedora-clang, r-devel-windows-x86_64-new-UL, r-release-macos-arm64, r-release-macos-x86_64, r-release-windows-ix86+x86_64, r-oldrel-macos-x86_64, r-oldrel-windows-ix86+x86_64

Version: 1.1-27.1
Check: tests
Result: ERROR
     Running ‘AAAtest-all.R’ [62s/88s]
     Running ‘HSAURtrees.R’
     Running ‘REMLdev.R’
     Running ‘ST.R’
     Running ‘agridat_gotway.R’
     Running ‘bootMer.R’ [10s/22s]
     Running ‘boundary.R’ [13s/17s]
     Running ‘confint.R’
     Running ‘devCritFun.R’
     Running ‘drop.R’
     Running ‘drop1contrasts.R’
     Running ‘dynload.R’
     Running ‘elston.R’
     Running ‘evalCall.R’
     Running ‘extras.R’
     Running ‘falsezero_dorie.R’
     Running ‘fewlevels.R’
     Running ‘getME.R’
     Running ‘glmer-1.R’
     Running ‘glmerControlPass.R’
     Running ‘glmerWarn.R’
     Running ‘glmmExt.R’ [12s/14s]
     Running ‘glmmWeights.R’ [11s/14s]
     Running ‘hatvalues.R’
     Running ‘is.R’
     Running ‘lmList-tst.R’
     Running ‘lme4_nlme.R’
     Running ‘lmer-0.R’
     Running ‘lmer-1.R’
     Comparing ‘lmer-1.Rout’ to ‘lmer-1.Rout.save’ ... OK
     Running ‘lmer-conv.R’
     Running ‘lmer2_ex.R’
     Running ‘methods.R’
     Running ‘minval.R’
     Running ‘modFormula.R’
     Running ‘nbinom.R’
     Running ‘nlmer-conv.R’
     Running ‘nlmer.R’
     Comparing ‘nlmer.Rout’ to ‘nlmer.Rout.save’ ... OK
     Running ‘offset.R’
     Running ‘optimizer.R’
     Running ‘polytomous.R’
     Running ‘prLogistic.R’
     Running ‘predict_basis.R’
     Running ‘predsim.R’
     Running ‘priorWeights.R’ [11s/14s]
     Running ‘priorWeightsModComp.R’
     Running ‘profile-tst.R’
     Running ‘refit.R’
     Running ‘resids.R’
     Running ‘respiratory.R’ [11s/16s]
     Running ‘simulate.R’
     Running ‘testOptControl.R’
     Running ‘testcolonizer.R’
     Running ‘testcrab.R’ [13s/16s]
     Running ‘throw.R’
     Running ‘varcorr.R’
     Running ‘vcov-etc.R’
    Running the tests in ‘tests/offset.R’ failed.
    Complete output:
     > ## simple examples with offsets, to exercise methods etc.
     >
     > library(lme4)
     Loading required package: Matrix
     >
     > if (.Platform$OS.type != "windows") {
     + ## generate a basic Gamma/random effects sim
     + set.seed(101)
     + d <- expand.grid(block=LETTERS[1:26],rep=1:100)
     + d$x <- runif(nrow(d)) ## sd=1
     + reff_f <- rnorm(length(levels(d$block)),sd=1)
     + ## need intercept large enough to avoid negative values
     + d$eta0 <- 4+3*d$x ## version without random effects
     + d$eta <- d$eta0+reff_f[d$block]
     +
     + ## lmer() test:
     + d$mu <- d$eta
     + d$y <- rnorm(nrow(d),mean=d$mu,sd=1)
     +
     + fm1 <- lmer(y~x+(1|block),data=d)
     + fm1off <- lmer(y~x+(1|block)+offset(3*x),data=d)
     +
     + ## check equality
     + stopifnot(all.equal(fixef(fm1)[2]-3,fixef(fm1off)[2]))
     +
     + p0 <- predict(fm1)
     + p1 <- predict(fm1,newdata=d)
     + p2 <- predict(fm1off,newdata=d)
     + stopifnot(all.equal(p0,p1,p2))
     +
     +
     + ## glmer() test:
     + d$mu <- exp(d$eta)
     + d$y <- rpois(nrow(d),d$mu)
     +
     + gm1 <- glmer(y~x+(1|block),data=d,family=poisson,
     + control=glmerControl(check.conv.grad="ignore"))
     + gm1off <- glmer(y~x+(1|block)+offset(3*x),data=d,family=poisson,
     + control=glmerControl(check.conv.grad="ignore"))
     +
     + ## check equality
     + stopifnot(all.equal(fixef(gm1)[2]-3,fixef(gm1off)[2],tolerance=3e-4))
     +
     + p0 <- predict(gm1)
     + p1 <- predict(gm1,newdata=d)
     + p2 <- predict(gm1off,newdata=d)
     + stopifnot(all.equal(p0,p1,p2))
     +
     + ## FIXME: should also test simulations
     + } ## skip on windows (for speed)
     Error in all.equal.numeric(p0, p1, p2) :
     length(tolerance) == 1L is not TRUE
     Calls: stopifnot ... all.equal -> all.equal -> all.equal.numeric -> stopifnot
     Execution halted
Flavor: r-devel-linux-x86_64-fedora-clang

Version: 1.1-27.1
Check: tests
Result: ERROR
     Running ‘AAAtest-all.R’ [65s/77s]
     Running ‘HSAURtrees.R’
     Running ‘REMLdev.R’
     Running ‘ST.R’
     Running ‘agridat_gotway.R’
     Running ‘bootMer.R’ [11s/21s]
     Running ‘boundary.R’ [15s/15s]
     Running ‘confint.R’
     Running ‘devCritFun.R’
     Running ‘drop.R’
     Running ‘drop1contrasts.R’
     Running ‘dynload.R’ [10s/14s]
     Running ‘elston.R’
     Running ‘evalCall.R’
     Running ‘extras.R’
     Running ‘falsezero_dorie.R’
     Running ‘fewlevels.R’
     Running ‘getME.R’
     Running ‘glmer-1.R’
     Running ‘glmerControlPass.R’ [9s/13s]
     Running ‘glmerWarn.R’
     Running ‘glmmExt.R’ [12s/15s]
     Running ‘glmmWeights.R’ [11s/14s]
     Running ‘hatvalues.R’
     Running ‘is.R’
     Running ‘lmList-tst.R’
     Running ‘lme4_nlme.R’
     Running ‘lmer-0.R’
     Running ‘lmer-1.R’
     Comparing ‘lmer-1.Rout’ to ‘lmer-1.Rout.save’ ... OK
     Running ‘lmer-conv.R’
     Running ‘lmer2_ex.R’
     Running ‘methods.R’
     Running ‘minval.R’
     Running ‘modFormula.R’
     Running ‘nbinom.R’
     Running ‘nlmer-conv.R’
     Running ‘nlmer.R’
     Comparing ‘nlmer.Rout’ to ‘nlmer.Rout.save’ ... OK
     Running ‘offset.R’
     Running ‘optimizer.R’ [7s/10s]
     Running ‘polytomous.R’
     Running ‘prLogistic.R’
     Running ‘predict_basis.R’
     Running ‘predsim.R’
     Running ‘priorWeights.R’ [11s/14s]
     Running ‘priorWeightsModComp.R’
     Running ‘profile-tst.R’
     Running ‘refit.R’
     Running ‘resids.R’
     Running ‘respiratory.R’ [12s/13s]
     Running ‘simulate.R’
     Running ‘testOptControl.R’
     Running ‘testcolonizer.R’
     Running ‘testcrab.R’ [13s/13s]
     Running ‘throw.R’
     Running ‘varcorr.R’
     Running ‘vcov-etc.R’
    Running the tests in ‘tests/offset.R’ failed.
    Complete output:
     > ## simple examples with offsets, to exercise methods etc.
     >
     > library(lme4)
     Loading required package: Matrix
     >
     > if (.Platform$OS.type != "windows") {
     + ## generate a basic Gamma/random effects sim
     + set.seed(101)
     + d <- expand.grid(block=LETTERS[1:26],rep=1:100)
     + d$x <- runif(nrow(d)) ## sd=1
     + reff_f <- rnorm(length(levels(d$block)),sd=1)
     + ## need intercept large enough to avoid negative values
     + d$eta0 <- 4+3*d$x ## version without random effects
     + d$eta <- d$eta0+reff_f[d$block]
     +
     + ## lmer() test:
     + d$mu <- d$eta
     + d$y <- rnorm(nrow(d),mean=d$mu,sd=1)
     +
     + fm1 <- lmer(y~x+(1|block),data=d)
     + fm1off <- lmer(y~x+(1|block)+offset(3*x),data=d)
     +
     + ## check equality
     + stopifnot(all.equal(fixef(fm1)[2]-3,fixef(fm1off)[2]))
     +
     + p0 <- predict(fm1)
     + p1 <- predict(fm1,newdata=d)
     + p2 <- predict(fm1off,newdata=d)
     + stopifnot(all.equal(p0,p1,p2))
     +
     +
     + ## glmer() test:
     + d$mu <- exp(d$eta)
     + d$y <- rpois(nrow(d),d$mu)
     +
     + gm1 <- glmer(y~x+(1|block),data=d,family=poisson,
     + control=glmerControl(check.conv.grad="ignore"))
     + gm1off <- glmer(y~x+(1|block)+offset(3*x),data=d,family=poisson,
     + control=glmerControl(check.conv.grad="ignore"))
     +
     + ## check equality
     + stopifnot(all.equal(fixef(gm1)[2]-3,fixef(gm1off)[2],tolerance=3e-4))
     +
     + p0 <- predict(gm1)
     + p1 <- predict(gm1,newdata=d)
     + p2 <- predict(gm1off,newdata=d)
     + stopifnot(all.equal(p0,p1,p2))
     +
     + ## FIXME: should also test simulations
     + } ## skip on windows (for speed)
     Error in all.equal.numeric(p0, p1, p2) :
     length(tolerance) == 1L is not TRUE
     Calls: stopifnot ... all.equal -> all.equal -> all.equal.numeric -> stopifnot
     Execution halted
Flavor: r-devel-linux-x86_64-fedora-gcc

Version: 1.1-27.1
Check: package dependencies
Result: ERROR
    Package required but not available: 'nloptr'
    
    Packages suggested but not available for checking:
     'MEMSS', 'mlmRev', 'gamm4', 'pbkrtest', 'car', 'rr2', 'semEff'
    
    See section 'The DESCRIPTION file' in the 'Writing R Extensions'
    manual.
Flavor: r-devel-windows-x86_64-new-TK