CRAN Package Check Results for Package qra

Last updated on 2021-07-08 07:49:38 CEST.

Flavor Version Tinstall Tcheck Ttotal Status Flags
r-devel-linux-x86_64-debian-clang 0.1.8 12.80 313.71 326.51 OK
r-devel-linux-x86_64-debian-gcc 0.1.8 9.36 240.85 250.21 OK
r-devel-linux-x86_64-fedora-clang 0.1.8 387.68 NOTE
r-devel-linux-x86_64-fedora-gcc 0.1.8 395.60 OK
r-devel-windows-x86_64 0.1.8 17.00 411.00 428.00 OK
r-devel-windows-x86_64-gcc10-UCRT 0.1.8 OK
r-patched-linux-x86_64 0.1.8 11.67 301.09 312.76 OK
r-patched-solaris-x86 0.1.8 217.60 ERROR
r-release-linux-x86_64 0.1.8 11.08 303.84 314.92 OK
r-release-macos-arm64 0.1.8 OK
r-release-macos-x86_64 0.1.8 OK
r-release-windows-ix86+x86_64 0.1.8 17.00 410.00 427.00 OK
r-oldrel-macos-x86_64 0.1.8 WARN
r-oldrel-windows-ix86+x86_64 0.1.8 26.00 411.00 437.00 OK

Check Details

Version: 0.1.8
Check: Rd cross-references
Result: NOTE
    Undeclared package ‘DAAG’ in Rd xrefs
Flavor: r-devel-linux-x86_64-fedora-clang

Version: 0.1.8
Check: package dependencies
Result: NOTE
    Package suggested but not available for checking: ‘glmmTMB’
Flavor: r-patched-solaris-x86

Version: 0.1.8
Check: examples
Result: ERROR
    Running examples in ‘qra-Ex.R’ failed
    The error most likely occurred in:
    
    > ### Name: extractLT
    > ### Title: Obtain complete set of LT or LD estimates
    > ### Aliases: extractLT extractLTpwr
    >
    > ### ** Examples
    >
    > form <- cbind(dead,total-dead)~0+Cultivar/dose+(1|cultRep)
    > codling1989.TMB <- glmmTMB::glmmTMB(formula=form,
    + family=glmmTMB::betabinomial(link='cloglog'),
    + dispformula=~0+Cultivar/splines::ns(dose,2),
    + data=subset(codling1989,dose>0))
    Error in loadNamespace(x) : there is no package called ‘glmmTMB’
    Calls: loadNamespace -> withRestarts -> withOneRestart -> doWithOneRestart
    Execution halted
Flavor: r-patched-solaris-x86

Version: 0.1.8
Check: re-building of vignette outputs
Result: WARN
    Error(s) in re-building vignettes:
     ...
    --- re-building ‘MeBrPlot.Rmd’ using rmarkdown
    Warning in engine$weave(file, quiet = quiet, encoding = enc) :
     Pandoc (>= 1.12.3) not available. Falling back to R Markdown v1.
    Quitting from lines 13-16 (MeBrPlot.Rmd)
    Error: processing vignette 'MeBrPlot.Rmd' failed with diagnostics:
    there is no package called 'glmmTMB'
    --- failed re-building ‘MeBrPlot.Rmd’
    
    --- re-building ‘countDists.Rmd’ using rmarkdown
    Warning in engine$weave(file, quiet = quiet, encoding = enc) :
     Pandoc (>= 1.12.3) not available. Falling back to R Markdown v1.
    The magick package is required to crop "figure/plot-gph12-1.png" but not available.
    The magick package is required to crop "figure/cfDBI-BB-1.png" but not available.
    The magick package is required to crop "figure/plot-binAB-1.png" but not available.
    The magick package is required to crop "figure/cfsim-1.png" but not available.
    The magick package is required to crop "figure/cfq2-1.png" but not available.
    The magick package is required to crop "figure/rqmales-1.png" but not available.
    The magick package is required to crop "figure/plot-poisAB-1.png" but not available.
    The magick package is required to crop "figure/wormpois-1.png" but not available.
    --- finished re-building ‘countDists.Rmd’
    
    --- re-building ‘timeMortality.Rmd’ using rmarkdown
    Warning in engine$weave(file, quiet = quiet, encoding = enc) :
     Pandoc (>= 1.12.3) not available. Falling back to R Markdown v1.
    Quitting from lines 237-251 (timeMortality.Rmd)
    Error: processing vignette 'timeMortality.Rmd' failed with diagnostics:
    there is no package called 'glmmTMB'
    --- failed re-building ‘timeMortality.Rmd’
    
    SUMMARY: processing the following files failed:
     ‘MeBrPlot.Rmd’ ‘timeMortality.Rmd’
    
    Error: Vignette re-building failed.
    Execution halted
Flavor: r-patched-solaris-x86

Version: 0.1.8
Check: re-building of vignette outputs
Result: WARN
    Error(s) in re-building vignettes:
    --- re-building ‘MeBrPlot.Rmd’ using rmarkdown
    Warning in engine$weave(file, quiet = quiet, encoding = enc) :
     Pandoc (>= 1.12.3) not available. Falling back to R Markdown v1.
    Error in .Call("FreeADFunObject", ptr, PACKAGE = DLL) :
     "FreeADFunObject" not available for .Call() for package "glmmTMB"
    Calls: <Anonymous>
    Error in .Call("FreeADFunObject", ptr, PACKAGE = DLL) :
     "FreeADFunObject" not available for .Call() for package "glmmTMB"
    Calls: <Anonymous>
    Error in .Call("FreeADFunObject", ptr, PACKAGE = DLL) :
     "FreeADFunObject" not available for .Call() for package "glmmTMB"
    Calls: <Anonymous>
    Error in .Call("FreeADFunObject", ptr, PACKAGE = DLL) :
     "FreeADFunObject" not available for .Call() for package "glmmTMB"
    Calls: <Anonymous>
    Error in .Call("FreeADFunObject", ptr, PACKAGE = DLL) :
     "FreeADFunObject" not available for .Call() for package "glmmTMB"
    Calls: <Anonymous>
    Error in .Call("FreeADFunObject", ptr, PACKAGE = DLL) :
     "FreeADFunObject" not available for .Call() for package "glmmTMB"
    Calls: <Anonymous>
    Error in .Call("FreeADFunObject", ptr, PACKAGE = DLL) :
     "FreeADFunObject" not available for .Call() for package "glmmTMB"
    Calls: <Anonymous>
    Error in .Call("FreeADFunObject", ptr, PACKAGE = DLL) :
     "FreeADFunObject" not available for .Call() for package "glmmTMB"
    Calls: <Anonymous>
    Error in .Call("FreeADFunObject", ptr, PACKAGE = DLL) :
     "FreeADFunObject" not available for .Call() for package "glmmTMB"
    Calls: <Anonymous>
    Error in .Call("FreeADFunObject", ptr, PACKAGE = DLL) :
     "FreeADFunObject" not available for .Call() for package "glmmTMB"
    Calls: <Anonymous>
    Error in .Call("FreeADFunObject", ptr, PACKAGE = DLL) :
     "FreeADFunObject" not available for .Call() for package "glmmTMB"
    Calls: <Anonymous>
    Error in .Call("FreeADFunObject", ptr, PACKAGE = DLL) :
     "FreeADFunObject" not available for .Call() for package "glmmTMB"
    Calls: <Anonymous>
    Error in .Call("FreeADFunObject", ptr, PACKAGE = DLL) :
     "FreeADFunObject" not available for .Call() for package "glmmTMB"
    Calls: <Anonymous>
    Error in .Call("FreeADFunObject", ptr, PACKAGE = DLL) :
     "FreeADFunObject" not available for .Call() for package "glmmTMB"
    Calls: <Anonymous>
    Error in .Call("FreeADFunObject", ptr, PACKAGE = DLL) :
     "FreeADFunObject" not available for .Call() for package "glmmTMB"
    Calls: <Anonymous>
    Error in .Call("FreeADFunObject", ptr, PACKAGE = DLL) :
     "FreeADFunObject" not available for .Call() for package "glmmTMB"
    Calls: <Anonymous>
    Error in .Call("FreeADFunObject", ptr, PACKAGE = DLL) :
     "FreeADFunObject" not available for .Call() for package "glmmTMB"
    Calls: <Anonymous>
    Error in .Call("FreeADFunObject", ptr, PACKAGE = DLL) :
     "FreeADFunObject" not available for .Call() for package "glmmTMB"
    Calls: <Anonymous>
    Error in .Call("FreeADFunObject", ptr, PACKAGE = DLL) :
     "FreeADFunObject" not available for .Call() for package "glmmTMB"
    Calls: <Anonymous>
    Error in .Call("FreeADFunObject", ptr, PACKAGE = DLL) :
     "FreeADFunObject" not available for .Call() for package "glmmTMB"
    Calls: <Anonymous>
    Error in .Call("FreeADFunObject", ptr, PACKAGE = DLL) :
     "FreeADFunObject" not available for .Call() for package "glmmTMB"
    Calls: <Anonymous>
    --- finished re-building ‘MeBrPlot.Rmd’
    
    --- re-building ‘countDists.Rmd’ using rmarkdown
    Warning in engine$weave(file, quiet = quiet, encoding = enc) :
     Pandoc (>= 1.12.3) not available. Falling back to R Markdown v1.
    --- finished re-building ‘countDists.Rmd’
    
    --- re-building ‘timeMortality.Rmd’ using rmarkdown
    Warning in engine$weave(file, quiet = quiet, encoding = enc) :
     Pandoc (>= 1.12.3) not available. Falling back to R Markdown v1.
    Warning in checkMatrixPackageVersion() :
     Package version inconsistency detected.
    TMB was built with Matrix version 1.3.2
    Current Matrix version is 1.3.4
    Please re-install 'TMB' from source using install.packages('TMB', type = 'source') or ask CRAN for a binary version of 'TMB' matching CRAN's 'Matrix' package
    Warning in Matrix::sparseMatrix(dims = c(0, 0), i = integer(0), j = integer(0), :
     'giveCsparse' has been deprecated; setting 'repr = "T"' for you
    Warning in Matrix::sparseMatrix(dims = c(0, 0), i = integer(0), j = integer(0), :
     'giveCsparse' has been deprecated; setting 'repr = "T"' for you
    Warning in Matrix::sparseMatrix(dims = c(0, 0), i = integer(0), j = integer(0), :
     'giveCsparse' has been deprecated; setting 'repr = "T"' for you
    Error in .Call("FreeADFunObject", ptr, PACKAGE = DLL) :
     "FreeADFunObject" not available for .Call() for package "glmmTMB"
    Calls: <Anonymous>
    Warning in (function (start, objective, gradient = NULL, hessian = NULL, :
     NA/NaN function evaluation
    Warning in (function (start, objective, gradient = NULL, hessian = NULL, :
     NA/NaN function evaluation
    Warning in (function (start, objective, gradient = NULL, hessian = NULL, :
     NA/NaN function evaluation
    Warning in (function (start, objective, gradient = NULL, hessian = NULL, :
     NA/NaN function evaluation
    Warning in (function (start, objective, gradient = NULL, hessian = NULL, :
     NA/NaN function evaluation
    Warning in (function (start, objective, gradient = NULL, hessian = NULL, :
     NA/NaN function evaluation
    Warning in Matrix::sparseMatrix(dims = c(0, 0), i = integer(0), j = integer(0), :
     'giveCsparse' has been deprecated; setting 'repr = "T"' for you
    Warning in Matrix::sparseMatrix(dims = c(0, 0), i = integer(0), j = integer(0), :
     'giveCsparse' has been deprecated; setting 'repr = "T"' for you
    Warning in Matrix::sparseMatrix(dims = c(0, 0), i = integer(0), j = integer(0), :
     'giveCsparse' has been deprecated; setting 'repr = "T"' for you
    Error in .Call("FreeADFunObject", ptr, PACKAGE = DLL) :
     "FreeADFunObject" not available for .Call() for package "glmmTMB"
    Calls: <Anonymous>
    Error in .Call("FreeADFunObject", ptr, PACKAGE = DLL) :
     "FreeADFunObject" not available for .Call() for package "glmmTMB"
    Calls: <Anonymous>
    Warning in (function (start, objective, gradient = NULL, hessian = NULL, :
     NA/NaN function evaluation
    Warning in (function (start, objective, gradient = NULL, hessian = NULL, :
     NA/NaN function evaluation
    Warning in (function (start, objective, gradient = NULL, hessian = NULL, :
     NA/NaN function evaluation
    Warning in (function (start, objective, gradient = NULL, hessian = NULL, :
     NA/NaN function evaluation
    Warning in (function (start, objective, gradient = NULL, hessian = NULL, :
     NA/NaN function evaluation
    Warning in (function (start, objective, gradient = NULL, hessian = NULL, :
     NA/NaN function evaluation
    Warning in (function (start, objective, gradient = NULL, hessian = NULL, :
     NA/NaN function evaluation
    Warning in fitTMB(TMBStruc) :
     Model convergence problem; non-positive-definite Hessian matrix. See vignette('troubleshooting')
    Warning in Matrix::sparseMatrix(dims = c(0, 0), i = integer(0), j = integer(0), :
     'giveCsparse' has been deprecated; setting 'repr = "T"' for you
    Warning in Matrix::sparseMatrix(dims = c(0, 0), i = integer(0), j = integer(0), :
     'giveCsparse' has been deprecated; setting 'repr = "T"' for you
    Warning in Matrix::sparseMatrix(dims = c(0, 0), i = integer(0), j = integer(0), :
     'giveCsparse' has been deprecated; setting 'repr = "T"' for you
    Error in .Call("FreeADFunObject", ptr, PACKAGE = DLL) :
     "FreeADFunObject" not available for .Call() for package "glmmTMB"
    Calls: <Anonymous>
    Error in .Call("FreeADFunObject", ptr, PACKAGE = DLL) :
     "FreeADFunObject" not available for .Call() for package "glmmTMB"
    Calls: <Anonymous>
    Warning in Matrix::sparseMatrix(dims = c(0, 0), i = integer(0), j = integer(0), :
     'giveCsparse' has been deprecated; setting 'repr = "T"' for you
    Warning in Matrix::sparseMatrix(dims = c(0, 0), i = integer(0), j = integer(0), :
     'giveCsparse' has been deprecated; setting 'repr = "T"' for you
    Warning in Matrix::sparseMatrix(dims = c(0, 0), i = integer(0), j = integer(0), :
     'giveCsparse' has been deprecated; setting 'repr = "T"' for you
    Error in .Call("FreeADFunObject", ptr, PACKAGE = DLL) :
     "FreeADFunObject" not available for .Call() for package "glmmTMB"
    Calls: <Anonymous>
    Error in .Call("FreeADFunObject", ptr, PACKAGE = DLL) :
     "FreeADFunObject" not available for .Call() for package "glmmTMB"
    Calls: <Anonymous>
    Warning in fitTMB(TMBStruc) :
     Model convergence problem; non-positive-definite Hessian matrix. See vignette('troubleshooting')
    Error in .Call("FreeADFunObject", ptr, PACKAGE = DLL) :
     "FreeADFunObject" not available for .Call() for package "glmmTMB"
    Calls: <Anonymous>
    Error in .Call("FreeADFunObject", ptr, PACKAGE = DLL) :
     "FreeADFunObject" not available for .Call() for package "glmmTMB"
    Calls: <Anonymous>
    Error in .Call("FreeADFunObject", ptr, PACKAGE = DLL) :
     "FreeADFunObject" not available for .Call() for package "glmmTMB"
    Calls: <Anonymous>
    Error in .Call("FreeADFunObject", ptr, PACKAGE = DLL) :
     "FreeADFunObject" not available for .Call() for package "glmmTMB"
    Calls: <Anonymous>
    Error in .Call("FreeADFunObject", ptr, PACKAGE = DLL) :
     "FreeADFunObject" not available for .Call() for package "glmmTMB"
    Calls: <Anonymous>
    Error in .Call("FreeADFunObject", ptr, PACKAGE = DLL) :
     "FreeADFunObject" not available for .Call() for package "glmmTMB"
    Calls: <Anonymous>
    Error in .Call("FreeADFunObject", ptr, PACKAGE = DLL) :
     "FreeADFunObject" not available for .Call() for package "glmmTMB"
    Calls: <Anonymous>
    Error in .Call("FreeADFunObject", ptr, PACKAGE = DLL) :
     "FreeADFunObject" not available for .Call() for package "glmmTMB"
    Calls: <Anonymous>
    Error in .Call("FreeADFunObject", ptr, PACKAGE = DLL) :
     "FreeADFunObject" not available for .Call() for package "glmmTMB"
    Calls: <Anonymous>
    Error in .Call("FreeADFunObject", ptr, PACKAGE = DLL) :
     "FreeADFunObject" not available for .Call() for package "glmmTMB"
    Calls: <Anonymous>
    Error in .Call("FreeADFunObject", ptr, PACKAGE = DLL) :
     "FreeADFunObject" not available for .Call() for package "glmmTMB"
    Calls: <Anonymous>
    Error in .Call("FreeADFunObject", ptr, PACKAGE = DLL) :
     "FreeADFunObject" not available for .Call() for package "glmmTMB"
    Calls: <Anonymous>
    Error in .Call("FreeADFunObject", ptr, PACKAGE = DLL) :
     "FreeADFunObject" not available for .Call() for package "glmmTMB"
    Calls: <Anonymous>
    Error in .Call("FreeADFunObject", ptr, PACKAGE = DLL) :
     "FreeADFunObject" not available for .Call() for package "glmmTMB"
    Calls: <Anonymous>
    Error in .Call("FreeADFunObject", ptr, PACKAGE = DLL) :
     "FreeADFunObject" not available for .Call() for package "glmmTMB"
    Calls: <Anonymous>
    Error in .Call("FreeADFunObject", ptr, PACKAGE = DLL) :
     "FreeADFunObject" not available for .Call() for package "glmmTMB"
    Calls: <Anonymous>
    Error in .Call("FreeADFunObject", ptr, PACKAGE = DLL) :
     "FreeADFunObject" not available for .Call() for package "glmmTMB"
    Calls: <Anonymous>
    Error in .Call("FreeADFunObject", ptr, PACKAGE = DLL) :
     "FreeADFunObject" not available for .Call() for package "glmmTMB"
    Calls: <Anonymous>
    Error in .Call("FreeADFunObject", ptr, PACKAGE = DLL) :
     "FreeADFunObject" not available for .Call() for package "glmmTMB"
    Calls: <Anonymous>
    Error in .Call("FreeADFunObject", ptr, PACKAGE = DLL) :
     "FreeADFunObject" not available for .Call() for package "glmmTMB"
    Calls: <Anonymous>
    Error in .Call("FreeADFunObject", ptr, PACKAGE = DLL) :
     "FreeADFunObject" not available for .Call() for package "glmmTMB"
    Calls: <Anonymous>
    Error in .Call("FreeADFunObject", ptr, PACKAGE = DLL) :
     "FreeADFunObject" not available for .Call() for package "glmmTMB"
    Calls: <Anonymous>
    Error in .Call("FreeADFunObject", ptr, PACKAGE = DLL) :
     "FreeADFunObject" not available for .Call() for package "glmmTMB"
    Calls: <Anonymous>
    Error in .Call("FreeADFunObject", ptr, PACKAGE = DLL) :
     "FreeADFunObject" not available for .Call() for package "glmmTMB"
    Calls: <Anonymous>
    Error in .Call("FreeADFunObject", ptr, PACKAGE = DLL) :
     "FreeADFunObject" not available for .Call() for package "glmmTMB"
    Calls: <Anonymous>
    Error in .Call("FreeADFunObject", ptr, PACKAGE = DLL) :
     "FreeADFunObject" not available for .Call() for package "glmmTMB"
    Calls: <Anonymous>
    Error in .Call("FreeADFunObject", ptr, PACKAGE = DLL) :
     "FreeADFunObject" not available for .Call() for package "glmmTMB"
    Calls: <Anonymous>
    Error in .Call("FreeADFunObject", ptr, PACKAGE = DLL) :
     "FreeADFunObject" not available for .Call() for package "glmmTMB"
    Calls: <Anonymous>
    Error in .Call("FreeADFunObject", ptr, PACKAGE = DLL) :
     "FreeADFunObject" not available for .Call() for package "glmmTMB"
    Calls: <Anonymous>
    Quitting from lines 334-384 (timeMortality.Rmd)
    Error: processing vignette 'timeMortality.Rmd' failed with diagnostics:
    cannot pop the top-level viewport ('grid' and 'graphics' output mixed?)
    --- failed re-building ‘timeMortality.Rmd’
    
    SUMMARY: processing the following file failed:
     ‘timeMortality.Rmd’
    
    Error: Vignette re-building failed.
    Execution halted
Flavor: r-oldrel-macos-x86_64