CRAN Package Check Results for Package lme4

Last updated on 2015-04-19 11:51:11.

Flavor Version Tinstall Tcheck Ttotal Status Flags
r-devel-linux-x86_64-debian-clang 1.1-7 42.05 345.56 387.61 WARN
r-devel-linux-x86_64-debian-gcc 1.1-7 42.44 345.83 388.27 WARN
r-devel-linux-x86_64-fedora-clang 1.1-7 796.53 WARN
r-devel-linux-x86_64-fedora-gcc 1.1-7 768.85 WARN
r-devel-osx-x86_64-clang 1.1-7 601.35 WARN
r-devel-windows-ix86+x86_64 1.1-7 115.00 861.00 976.00 WARN
r-patched-linux-x86_64 1.1-7 44.49 347.48 391.97 WARN
r-patched-solaris-sparc 1.1-7 4852.00 ERROR
r-patched-solaris-x86 1.1-7 953.60 NOTE
r-release-linux-x86_64 1.1-7 43.41 350.48 393.88 WARN
r-release-osx-x86_64-mavericks 1.1-7 ERROR
r-release-osx-x86_64-snowleopard 1.1-7 ERROR
r-release-windows-ix86+x86_64 1.1-7 105.00 793.00 898.00 WARN
r-oldrel-windows-ix86+x86_64 1.1-7 143.00 1199.00 1342.00 NOTE

Memtest notes: UBSAN-gcc UBSAN-gcc

Check Details

Version: 1.1-7
Check: installed package size
Result: NOTE
     installed size is 23.1Mb
     sub-directories of 1Mb or more:
     doc 1.3Mb
     libs 18.9Mb
Flavors: r-devel-linux-x86_64-debian-clang, r-devel-linux-x86_64-debian-gcc, r-devel-linux-x86_64-fedora-clang, r-devel-linux-x86_64-fedora-gcc, r-devel-windows-ix86+x86_64, r-patched-linux-x86_64, r-patched-solaris-sparc, r-patched-solaris-x86, r-release-linux-x86_64, r-release-osx-x86_64-mavericks, r-release-windows-ix86+x86_64, r-oldrel-windows-ix86+x86_64

Version: 1.1-7
Check: use of S3 registration
Result: WARN
    Registered S3 methods from standard package(s) overwritten by 'lme4':
     method from
     coef.lmList nlme
     formula.lmList nlme
     update.lmList nlme
Flavors: r-devel-linux-x86_64-debian-clang, r-devel-linux-x86_64-debian-gcc, r-devel-linux-x86_64-fedora-clang, r-devel-linux-x86_64-fedora-gcc, r-devel-osx-x86_64-clang, r-devel-windows-ix86+x86_64, r-devel-windows-ix86+x86_64, r-patched-linux-x86_64, r-release-linux-x86_64, r-release-windows-ix86+x86_64, r-release-windows-ix86+x86_64

Version: 1.1-7
Check: R code for possible problems
Result: NOTE
    GQdk: no visible binding for global variable ‘GQN’
    vcov.merMod : calc.vcov.hess: no visible global function definition for
     ‘forceSymmetric’
Flavors: r-devel-linux-x86_64-debian-clang, r-devel-linux-x86_64-debian-gcc, r-devel-linux-x86_64-fedora-clang, r-devel-linux-x86_64-fedora-gcc, r-devel-osx-x86_64-clang, r-devel-windows-ix86+x86_64, r-patched-linux-x86_64, r-patched-solaris-sparc, r-patched-solaris-x86, r-release-linux-x86_64, r-release-osx-x86_64-mavericks, r-release-windows-ix86+x86_64, r-oldrel-windows-ix86+x86_64

Version: 1.1-7
Check: tests
Result: ERROR
    Running the tests in ‘tests/testOptControl.R’ failed.
    Last 13 lines of output:
     Loading required package: Rcpp
     > dat <- read.csv(system.file("testdata","dat20101314.csv",package="lme4"))
     > NMcopy <- lme4:::Nelder_Mead
     >
     > cc <- capture.output(lmer(y ~ (1|Operator)+(1|Part)+(1|Part:Operator), data=dat,
     + control=
     + lmerControl("NMcopy",
     + optCtrl= list(iprint=20))))
     > ## check that printing goes through step 140 twice and up to 240 once
     > findStep <- function(str,n) sum(grepl(paste0("^\\(NM\\) ",n,": "),cc))
     > stopifnot(findStep(cc,140)==2 && findStep(cc,240)==1)
     Error: findStep(cc, 140) == 2 && findStep(cc, 240) == 1 is not TRUE
     Execution halted
Flavor: r-patched-solaris-sparc

Version: 1.1-7
Check: package dependencies
Result: NOTE
    Packages suggested but not available for checking:
     ‘MEMSS’ ‘mlmRev’ ‘gamm4’ ‘pbkrtest’
Flavor: r-release-osx-x86_64-mavericks

Version: 1.1-7
Check: Rd cross-references
Result: NOTE
    Package unavailable to check Rd xrefs: ‘pbkrtest’
Flavor: r-release-osx-x86_64-mavericks

Version: 1.1-7
Check: tests
Result: ERROR
    Running the tests in ‘tests/AAAtest-all.R’ failed.
    Last 13 lines of output:
    
     Error: Test failures
     In addition: Warning messages:
     1: In deviance.merMod(fm1) :
     deviance() is deprecated for REML fits; use REMLcrit for the REML criterion or deviance(.,REML=FALSE) for deviance calculated at the REML fit
     2: In norm.inter(t, alpha) : extreme order statistics used as endpoints
     3: In norm.inter(t, alpha) : extreme order statistics used as endpoints
     4: In norm.inter(t, alpha) : extreme order statistics used as endpoints
     5: In norm.inter(t, alpha) : extreme order statistics used as endpoints
     6: In norm.inter(t, alpha) : extreme order statistics used as endpoints
     7: In norm.inter(t, alpha) : extreme order statistics used as endpoints
     8: In rm("Orthodont") : object 'Orthodont' not found
     Execution halted
Flavor: r-release-osx-x86_64-mavericks

Version: 1.1-7
Check: running R code from vignettes
Result: WARN
    Errors in running code in vignettes:
    when running code in ‘lmer.Rnw’
     ...
    + pwrss <- resp$wrss() + pp$sqrL(1)
    + sig <- sqr .... [TRUNCATED]
     Residual Subject
    27.374472 8.898746
    
    > library("gamm4")
    
     When sourcing ‘lmer.R’:
    Error: there is no package called ‘gamm4’
    Execution halted
Flavor: r-release-osx-x86_64-mavericks

Version: 1.1-7
Check: re-building of vignette outputs
Result: NOTE
    Error in re-building vignettes:
     ...
    Loading required package: Matrix
    Loading required package: Rcpp
    Computing profile confidence intervals ...
    Computing bootstrap confidence intervals ...
    Quitting from lines 3091-3113 (lmer.Rnw)
    Error: processing vignette 'lmer.Rnw' failed with diagnostics:
    there is no package called 'gamm4'
    Execution halted
Flavor: r-release-osx-x86_64-mavericks

Version: 1.1-7
Check: package dependencies
Result: ERROR
    Packages suggested but not available for checking: ‘knitr’ ‘ggplot2’
    
    VignetteBuilder package required for checking but installed: ‘knitr’
    
    Files named as vignettes but with no recognized vignette engine:
     ‘inst/doc/lmer.Rnw’
    (Is a VignetteBuilder field missing?)
    
    See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
    manual.
Flavor: r-release-osx-x86_64-snowleopard