CRAN Package Check Results for Package lme4

Last updated on 2016-02-10 11:55:18.

Flavor Version Tinstall Tcheck Ttotal Status Flags
r-devel-linux-x86_64-debian-gcc 1.1-10 41.05 190.86 231.91 ERROR
r-devel-linux-x86_64-fedora-clang 1.1-10 468.68 ERROR
r-devel-linux-x86_64-fedora-gcc 1.1-10 453.36 ERROR
r-devel-osx-x86_64-clang 1.1-10 842.21 WARN
r-devel-windows-ix86+x86_64 1.1-10 177.00 730.00 907.00 ERROR
r-patched-linux-x86_64 1.1-10 41.38 198.48 239.87 ERROR
r-patched-solaris-sparc 1.1-10 5145.50 WARN
r-patched-solaris-x86 1.1-10 1020.30 WARN
r-release-linux-x86_64 1.1-10 41.77 197.38 239.15 ERROR
r-release-osx-x86_64-mavericks 1.1-10 NOTE
r-release-windows-ix86+x86_64 1.1-10 169.00 753.00 922.00 ERROR
r-oldrel-windows-ix86+x86_64 1.1-10 174.00 183.00 357.00 ERROR

Memtest notes: clang-UBSAN clang-UBSAN gcc6-UBSAN gcc6-UBSAN gcc-UBSAN gcc-UBSAN

Check Details

Version: 1.1-10
Check: installed package size
Result: NOTE
     installed size is 24.1Mb
     sub-directories of 1Mb or more:
     doc 1.8Mb
     libs 18.6Mb
     testdata 1.5Mb
Flavors: 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: 1.1-10
Check: S3 generic/method consistency
Result: WARN
    VarCorr:
     function(x, sigma, ...)
    VarCorr.merMod:
     function(x, sigma, rdig)
    
    See section ‘Generic functions and methods’ in the ‘Writing R
    Extensions’ manual.
Flavors: 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-windows-ix86+x86_64, r-oldrel-windows-ix86+x86_64

Version: 1.1-10
Check: tests
Result: ERROR
    Running the tests in ‘tests/AAAtest-all.R’ failed.
    Last 13 lines of output:
     2/2 mismatches (average diff: 3.3e-06).
     First 2:
     pos x y diff
     1 0.6301 0.6301 2.6e-06
     2 -0.0167 -0.0167 -4.0e-06
     Error: Test failures
     In addition: Warning messages:
     1: Placing tests in `inst/tests/` is deprecated. Please use `tests/testthat/` instead
     2: In checkConv(attr(opt, "derivs"), opt$par, ctrl = control$checkConv, :
     unable to evaluate scaled gradient
     3: In checkConv(attr(opt, "derivs"), opt$par, ctrl = control$checkConv, :
     Model failed to converge with max|grad| = 0.0469696 (tol = 0.001, component 1)
     Execution halted
Flavors: r-devel-linux-x86_64-debian-gcc, r-devel-linux-x86_64-fedora-clang, r-devel-linux-x86_64-fedora-gcc, r-patched-linux-x86_64

Version: 1.1-10
Check: running tests for arch ‘x64’
Result: ERROR
    Running the tests in 'tests/AAAtest-all.R' failed.
    Last 13 lines of output:
     2/2 mismatches (average diff: 3.3e-06).
     First 2:
     pos x y diff
     1 0.6301 0.6301 2.6e-06
     2 -0.0167 -0.0167 -4.0e-06
     Error: Test failures
     In addition: Warning messages:
     1: Placing tests in `inst/tests/` is deprecated. Please use `tests/testthat/` instead
     2: In checkConv(attr(opt, "derivs"), opt$par, ctrl = control$checkConv, :
     unable to evaluate scaled gradient
     3: In checkConv(attr(opt, "derivs"), opt$par, ctrl = control$checkConv, :
     Model failed to converge with max|grad| = 0.0469696 (tol = 0.001, component 1)
     Execution halted
Flavors: r-devel-windows-ix86+x86_64, r-release-windows-ix86+x86_64

Version: 1.1-10
Check: tests
Result: ERROR
    Running the tests in ‘tests/AAAtest-all.R’ failed.
    Last 13 lines of output:
     ....
     .summarizing/printing models :
     Utilities (including *non*-exported ones : .......................
    
     1. Failure (at test-methods.R#433): simulate -----------------------------------
     fixef(g1) not equal to c(`(Intercept)` = 0.630067, x = -0.0167248)
     2/2 mismatches (average diff: 3.3e-06).
     First 2:
     pos x y diff
     1 0.6301 0.6301 2.6e-06
     2 -0.0167 -0.0167 -4.0e-06
     Error: Test failures
     Execution halted
Flavor: r-release-linux-x86_64

Version: 1.1-10
Check: re-building of vignette outputs
Result: NOTE
    Error in re-building vignettes:
     ...
    Computing bootstrap confidence intervals ...
    Error in texi2dvi(file = file, pdf = TRUE, clean = clean, quiet = quiet, :
     Running 'texi2dvi' on 'lmer.tex' failed.
    LaTeX errors:
    ! Undefined control sequence.
    l.15 x<9c><ed>\Mh
     ^^TK^^P<ae><97>(q$<ee>؈!.L6^^L/($oYX^^Hx^^H<eb>!<a0>'o<de><<eb>ٓ^^A/<a2>O<f0>]ċ^^G<f5>^^]<84><e7>A...
    The control sequence at the end of the top line
    of your error message was never \def'ed. If you have
    ! LaTeX Error: Missing \begin{document}.
    
    See the LaTeX manual or LaTeX Companion for explanation.
    Type H <return> for immediate help.
     ...
    ! Missing $ inserted.
    <inserted text>
     $
    l.16 ...F<a0><ba>v<ed>Zggg<ad>V{<fd><fa>5^^Q9<8e>388866<a6><94><8a><e3>^^X<fd>^^]<c7><c1><83><ae>^
     <bd><9a>J<a5>l<db>v^^\^^G<9f>J<a9><87>^^O^^_<c6>q|...
    ! Extra }, or forgotten $.
    l.17 Ԓ<da>[}
     <b8>ӄ<f6><a0><9c>0^^L<89>(<9b><cd><e2>^^A<98><ce>0^^L<0b><85>^^BOm<b9>\^^^^^Z^^Z<8a><a2><88><a7>?<9b><cd>"@a<ce>0<8e>eYP{<a1>P<c0>O<<c8><e3>...
    I've deleted a group-closing
    Calls: buildVignettes -> texi2pdf -> texi2dvi
    Execution halted
Flavor: r-release-osx-x86_64-mavericks

Version: 1.1-10
Check: running examples for arch ‘i386’
Result: ERROR
    Running examples in 'lme4-Ex.R' failed
    The error most likely occurred in:
    
    > ### Name: drop1.merMod
    > ### Title: Drop all possible single fixed-effect terms from a mixed effect
    > ### model
    > ### Aliases: drop1.merMod
    > ### Keywords: misc
    >
    > ### ** Examples
    >
    > fm1 <- lmer(Reaction~Days+(Days|Subject),sleepstudy)
    > ## likelihood ratio tests
    > drop1(fm1,test="Chisq")
    Single term deletions
    
    Model:
    Reaction ~ Days + (Days | Subject)
     Df AIC LRT Pr(Chi)
    <none> 1763.9
    Days 1 1785.5 23.537 1.226e-06 ***
    ---
    Signif. codes: 0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1
    > ## use Kenward-Roger corrected F test, or parametric bootstrap,
    > ## to test the significance of each dropped predictor
    > if (require(pbkrtest) && packageVersion("pbkrtest")>="0.3.8") {
    + KRSumFun <- function(object, objectDrop, ...) {
    + krnames <- c("ndf","ddf","Fstat","p.value","F.scaling")
    + r <- if (missing(objectDrop)) {
    + setNames(rep(NA,length(krnames)),krnames)
    + } else {
    + krtest <- KRmodcomp(object,objectDrop)
    + unlist(krtest$stats[krnames])
    + }
    + attr(r,"method") <- c("Kenward-Roger via pbkrtest package")
    + r
    + }
    + drop1(fm1,test="user",sumFun=KRSumFun)
    +
    + if(lme4:::testLevel() >= 3) { ## takes about 16 sec
    + nsim <- 100
    + PBSumFun <- function(object, objectDrop, ...) {
    + pbnames <- c("stat","p.value")
    + r <- if (missing(objectDrop)) {
    + setNames(rep(NA,length(pbnames)),pbnames)
    + } else {
    + pbtest <- PBmodcomp(object,objectDrop,nsim=nsim)
    + unlist(pbtest$test[2,pbnames])
    + }
    + attr(r,"method") <- c("Parametric bootstrap via pbkrtest package")
    + r
    + }
    + system.time(drop1(fm1,test="user",sumFun=PBSumFun))
    + }
    + }
    Loading required package: pbkrtest
    Note: method with signature 'sparseMatrix#ANY' chosen for function 'kronecker',
     target signature 'dgCMatrix#ngCMatrix'.
     "ANY#sparseMatrix" would also be valid
    Error in cbind(do.call(cbind, SigmaG$G), X) :
     number of rows of matrices must match (see arg 2)
    Calls: drop1 ... vcovAdj -> vcovAdj.lmerMod -> vcovAdj16_internal -> cbind
    Execution halted
Flavor: r-oldrel-windows-ix86+x86_64

Version: 1.1-10
Check: running examples for arch ‘x64’
Result: ERROR
    Running examples in 'lme4-Ex.R' failed
    The error most likely occurred in:
    
    > ### Name: drop1.merMod
    > ### Title: Drop all possible single fixed-effect terms from a mixed effect
    > ### model
    > ### Aliases: drop1.merMod
    > ### Keywords: misc
    >
    > ### ** Examples
    >
    > fm1 <- lmer(Reaction~Days+(Days|Subject),sleepstudy)
    > ## likelihood ratio tests
    > drop1(fm1,test="Chisq")
    Single term deletions
    
    Model:
    Reaction ~ Days + (Days | Subject)
     Df AIC LRT Pr(Chi)
    <none> 1763.9
    Days 1 1785.5 23.537 1.226e-06 ***
    ---
    Signif. codes: 0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1
    > ## use Kenward-Roger corrected F test, or parametric bootstrap,
    > ## to test the significance of each dropped predictor
    > if (require(pbkrtest) && packageVersion("pbkrtest")>="0.3.8") {
    + KRSumFun <- function(object, objectDrop, ...) {
    + krnames <- c("ndf","ddf","Fstat","p.value","F.scaling")
    + r <- if (missing(objectDrop)) {
    + setNames(rep(NA,length(krnames)),krnames)
    + } else {
    + krtest <- KRmodcomp(object,objectDrop)
    + unlist(krtest$stats[krnames])
    + }
    + attr(r,"method") <- c("Kenward-Roger via pbkrtest package")
    + r
    + }
    + drop1(fm1,test="user",sumFun=KRSumFun)
    +
    + if(lme4:::testLevel() >= 3) { ## takes about 16 sec
    + nsim <- 100
    + PBSumFun <- function(object, objectDrop, ...) {
    + pbnames <- c("stat","p.value")
    + r <- if (missing(objectDrop)) {
    + setNames(rep(NA,length(pbnames)),pbnames)
    + } else {
    + pbtest <- PBmodcomp(object,objectDrop,nsim=nsim)
    + unlist(pbtest$test[2,pbnames])
    + }
    + attr(r,"method") <- c("Parametric bootstrap via pbkrtest package")
    + r
    + }
    + system.time(drop1(fm1,test="user",sumFun=PBSumFun))
    + }
    + }
    Loading required package: pbkrtest
    Note: method with signature 'sparseMatrix#ANY' chosen for function 'kronecker',
     target signature 'dgCMatrix#ngCMatrix'.
     "ANY#sparseMatrix" would also be valid
    Error in cbind(do.call(cbind, SigmaG$G), X) :
     number of rows of matrices must match (see arg 2)
    Calls: drop1 ... vcovAdj -> vcovAdj.lmerMod -> vcovAdj16_internal -> cbind
    Execution halted
Flavor: r-oldrel-windows-ix86+x86_64