• using R version 4.1.3 (2022-03-10)
• using platform: x86_64-w64-mingw32 (64-bit)
• using session charset: ISO8859-1
• checking for file 'mcglm/DESCRIPTION' ... OK
• checking extension type ... Package
• this is package 'mcglm' version '0.7.0'
• package encoding: UTF-8
• checking package namespace information ... OK
• checking package dependencies ... OK
• checking if this is a source package ... OK
• checking if there is a namespace ... OK
• checking for hidden files and directories ... OK
• checking for portable file names ... OK
• checking whether package 'mcglm' can be installed ... OK
• checking installed package size ... OK
• checking package directory ... OK
• checking 'build' directory ... OK
• checking DESCRIPTION meta-information ... OK
• checking top-level files ... OK
• checking for left-over files ... OK
• checking index information ... OK
• checking package subdirectories ... OK
• checking R files for non-ASCII characters ... OK
• checking R files for syntax errors ... OK
• loading checks for arch 'i386'
  ** checking whether the package can be loaded ... OK
  ** checking whether the package can be loaded with stated dependencies ... OK
  ** checking whether the package can be unloaded cleanly ... OK
  ** checking whether the namespace can be loaded with stated dependencies ... OK
  ** checking whether the namespace can be unloaded cleanly ... OK
  ** checking loading without being on the library search path ... OK
  ** checking use of S3 registration ... OK
• loading checks for arch 'x64'
  ** checking whether the package can be loaded ... OK
  ** checking whether the package can be loaded with stated dependencies ... OK
  ** checking whether the package can be unloaded cleanly ... OK
  ** checking whether the namespace can be loaded with stated dependencies ... OK
  ** checking whether the namespace can be unloaded cleanly ... OK
  ** checking loading without being on the library search path ... OK
  ** checking use of S3 registration ... OK
• checking dependencies in R code ... OK
• checking S3 generic/method consistency ... OK
• checking replacement functions ... OK
• checking foreign function calls ... OK
• checking R code for possible problems ... [17s] OK
• checking Rd files ... [1s] OK
• checking Rd metadata ... OK
• checking Rd cross-references ... OK
• checking for missing documentation entries ... OK
• checking for code/documentation mismatches ... OK
• checking Rd \usage sections ... OK
• checking Rd contents ... OK
• checking for unstated dependencies in examples ... OK
• checking contents of 'data' directory ... OK
• checking data for non-ASCII characters ... OK
• checking LazyData ... OK
• checking data for ASCII and uncompressed saves ... OK
• checking line endings in C/C++/Fortran sources/headers ... OK
• checking pragmas in C/C++ headers and code ... OK
• checking compiled code ... OK
• checking installed files from 'inst/doc' ... OK
• checking files in 'vignettes' ... OK
• checking examples ...
  ** running examples for arch 'i386' ... [4s] ERROR
  Running examples in 'mcglm-Ex.R' failed
  The error most likely occurred in:
  
  > ### Name: Hunting
  > ### Title: Hunting in Pico Basile, Bioko Island, Equatorial Guinea.
  > ### Aliases: Hunting
  > ### Keywords: datasets
  >
  > ### ** Examples
  >
  > library(mcglm)
  > library(Matrix)
  > data(Hunting, package="mcglm")
  > formu <- OT ~ METHOD*ALT + SEX + ALT*poly(MONTH, 4)
  > Z0 <- mc_id(Hunting)
  > Z1 <- mc_mixed(~0 + HUNTER.MONTH, data = Hunting)
  > fit <- mcglm(linear_pred = c(formu), matrix_pred = list(c(Z0, Z1)),
  + link = c("log"), variance = c("poisson_tweedie"),
  + power_fixed = c(FALSE),
  + control_algorithm = list(max_iter = 100),
  + offset = list(log(Hunting$OFFSET)), data = Hunting)
  Automatic initial values selected.
  Error in (function (classes, fdef, mtable) :
    unable to find an inherited method for function 'forceSymmetric' for signature '"dgCMatrix", "logical"'
  Error: $ operator is invalid for atomic vectors
  Execution halted
  ** running examples for arch 'x64' ... [4s] ERROR
  Running examples in 'mcglm-Ex.R' failed
  The error most likely occurred in:
  
  > ### Name: Hunting
  > ### Title: Hunting in Pico Basile, Bioko Island, Equatorial Guinea.
  > ### Aliases: Hunting
  > ### Keywords: datasets
  >
  > ### ** Examples
  >
  > library(mcglm)
  > library(Matrix)
  > data(Hunting, package="mcglm")
  > formu <- OT ~ METHOD*ALT + SEX + ALT*poly(MONTH, 4)
  > Z0 <- mc_id(Hunting)
  > Z1 <- mc_mixed(~0 + HUNTER.MONTH, data = Hunting)
  > fit <- mcglm(linear_pred = c(formu), matrix_pred = list(c(Z0, Z1)),
  + link = c("log"), variance = c("poisson_tweedie"),
  + power_fixed = c(FALSE),
  + control_algorithm = list(max_iter = 100),
  + offset = list(log(Hunting$OFFSET)), data = Hunting)
  Automatic initial values selected.
  Error in (function (classes, fdef, mtable) :
    unable to find an inherited method for function 'forceSymmetric' for signature '"dgCMatrix", "logical"'
  Error: $ operator is invalid for atomic vectors
  Execution halted
• checking for unstated dependencies in 'tests' ... OK
• checking tests ...
  ** running tests for arch 'i386' ... [11s] ERROR
    Running 'testthat.R' [11s]
  Running the tests in 'tests/testthat.R' failed.
  Complete output:
    > library(testthat)
    > library(mcglm)
    ----------------------------------------------------------------------
      mcglm: Multivariate Covariance Generalized Linear Models
    
      For support, collaboration or bug report, visit:
        http://mcglm.leg.ufpr.br/
    
      mcglm version 0.7.0 (build on 2021-07-07) is now loaded.
    ----------------------------------------------------------------------
    >
    > test_check("mcglm")
    [1] "Running test_mc_build_C.R"
    [1] "Testing covariance identity"
    [1] "OK"
    [1] "Testing covariance inverse"
    [1] "OK"
    [1] "Testing covariance expm"
    [1] "OK"
    [1] "Checking computations"
    [1] "Testing variance function: tweedie"
    [1] "OK"
    [1] "Testing variance function: binomialP"
    [1] "OK"
    [1] "Checking Poisson-Tweedie derivatives"
    [1] "Checking binomiaPQ derivatives"
    [1] "test_mc_build.C - OK"
    [1] "test_mc_build_omega.R"
    [1] "test_mc_build_omega.R - OK"
    [1] "test_mc_build_sigma.R"
    [1] "test_mc_build_sigma.R - OK"
    [1] "test_mc_build_sigma_between.R"
    [1] "test_mc_build_sigma_between.R-OK"
    [1] "Testing link functions ..."
    [1] "Testing link functions - Part II"
    [1] "Testing link functions - Part II"
    [1] "Testing Matrix linear predictor..."
    [1] "Testing Matrix linear predictor... OK"
    [1] "Testing variance function ..."
    [1] "Testing variance function ... OK"
    [ FAIL 1 | WARN 1 | SKIP 0 | PASS 370 ]
    
    == Failed tests ================================================================
    -- Error (test_mc_quasi_score.R:29:1): (code run outside of `test_that()`) -----
    Error in `(function (classes, fdef, mtable)
    {
        methods <- .findInheritedMethods(classes, fdef, mtable)
        if (length(methods) == 1L)
            return(methods[[1L]])
        else if (length(methods) == 0L) {
            cnames <- paste0("\"", vapply(classes, as.character,
                ""), "\"", collapse = ", ")
            stop(gettextf("unable to find an inherited method for function %s for signature %s",
                sQuote(fdef@generic), sQuote(cnames)), domain = NA)
        }
        else stop("Internal error in finding inherited methods; didn't return a unique method",
            domain = NA)
    })(list(structure("dgCMatrix", package = "Matrix"), "logical"),
        new("standardGeneric", .Data = function (x, uplo)
        standardGeneric("forceSymmetric"), generic = structure("forceSymmetric", package = "Matrix"),
            package = "Matrix", group = list(), valueClass = character(0),
            signature = c("x", "uplo"), default = NULL, skeleton = (function (x,
                uplo)
            stop(gettextf("invalid call in method dispatch to '%s' (no default method)",
                "forceSymmetric"), domain = NA))(x, uplo)), <environment>)`: unable to find an inherited method for function 'forceSymmetric' for signature '"dgCMatrix", "logical"'
    Backtrace:
        x
     1. \-mcglm:::mc_pearson(...) at test_mc_quasi_score.R:29:0
     2. \-mcglm:::mc_sensitivity(product, W = W)
     3. \-Matrix::forceSymmetric(Sensitivity, uplo = FALSE)
     4. \-methods (local) `<fn>`(`<list>`, `<stndrdGn>`, `<env>`)
    
    [ FAIL 1 | WARN 1 | SKIP 0 | PASS 370 ]
    Error: Test failures
    Execution halted
  ** running tests for arch 'x64' ... [12s] ERROR
    Running 'testthat.R' [12s]
  Running the tests in 'tests/testthat.R' failed.
  Complete output:
    > library(testthat)
    > library(mcglm)
    ----------------------------------------------------------------------
      mcglm: Multivariate Covariance Generalized Linear Models
    
      For support, collaboration or bug report, visit:
        http://mcglm.leg.ufpr.br/
    
      mcglm version 0.7.0 (build on 2021-07-07) is now loaded.
    ----------------------------------------------------------------------
    >
    > test_check("mcglm")
    [1] "Running test_mc_build_C.R"
    [1] "Testing covariance identity"
    [1] "OK"
    [1] "Testing covariance inverse"
    [1] "OK"
    [1] "Testing covariance expm"
    [1] "OK"
    [1] "Checking computations"
    [1] "Testing variance function: tweedie"
    [1] "OK"
    [1] "Testing variance function: binomialP"
    [1] "OK"
    [1] "Checking Poisson-Tweedie derivatives"
    [1] "Checking binomiaPQ derivatives"
    [1] "test_mc_build.C - OK"
    [1] "test_mc_build_omega.R"
    [1] "test_mc_build_omega.R - OK"
    [1] "test_mc_build_sigma.R"
    [1] "test_mc_build_sigma.R - OK"
    [1] "test_mc_build_sigma_between.R"
    [1] "test_mc_build_sigma_between.R-OK"
    [1] "Testing link functions ..."
    [1] "Testing link functions - Part II"
    [1] "Testing link functions - Part II"
    [1] "Testing Matrix linear predictor..."
    [1] "Testing Matrix linear predictor... OK"
    [1] "Testing variance function ..."
    [1] "Testing variance function ... OK"
    [ FAIL 1 | WARN 1 | SKIP 0 | PASS 370 ]
    
    == Failed tests ================================================================
    -- Error (test_mc_quasi_score.R:29:1): (code run outside of `test_that()`) -----
    Error in `(function (classes, fdef, mtable)
    {
        methods <- .findInheritedMethods(classes, fdef, mtable)
        if (length(methods) == 1L)
            return(methods[[1L]])
        else if (length(methods) == 0L) {
            cnames <- paste0("\"", vapply(classes, as.character,
                ""), "\"", collapse = ", ")
            stop(gettextf("unable to find an inherited method for function %s for signature %s",
                sQuote(fdef@generic), sQuote(cnames)), domain = NA)
        }
        else stop("Internal error in finding inherited methods; didn't return a unique method",
            domain = NA)
    })(list(structure("dgCMatrix", package = "Matrix"), "logical"),
        new("standardGeneric", .Data = function (x, uplo)
        standardGeneric("forceSymmetric"), generic = structure("forceSymmetric", package = "Matrix"),
            package = "Matrix", group = list(), valueClass = character(0),
            signature = c("x", "uplo"), default = NULL, skeleton = (function (x,
                uplo)
            stop(gettextf("invalid call in method dispatch to '%s' (no default method)",
                "forceSymmetric"), domain = NA))(x, uplo)), <environment>)`: unable to find an inherited method for function 'forceSymmetric' for signature '"dgCMatrix", "logical"'
    Backtrace:
        x
     1. \-mcglm:::mc_pearson(...) at test_mc_quasi_score.R:29:0
     2. \-mcglm:::mc_sensitivity(product, W = W)
     3. \-Matrix::forceSymmetric(Sensitivity, uplo = FALSE)
     4. \-methods (local) `<fn>`(`<list>`, `<stndrdGn>`, `<env>`)
    
    [ FAIL 1 | WARN 1 | SKIP 0 | PASS 370 ]
    Error: Test failures
    Execution halted
• checking for unstated dependencies in vignettes ... OK
• checking package vignettes in 'inst/doc' ... OK
• checking re-building of vignette outputs ... [9s] WARNING
  Error(s) in re-building vignettes:
  --- re-building 'GLMExamples.Rmd' using rmarkdown
  Loading required package: mcglm
  ----------------------------------------------------------------------
    mcglm: Multivariate Covariance Generalized Linear Models
  
    For support, collaboration or bug report, visit:
      http://mcglm.leg.ufpr.br/
  
    mcglm version 0.7.0 (build on 2021-07-07) is now loaded.
  ----------------------------------------------------------------------
  Loading required package: Matrix
  Quitting from lines 67-77 (GLMExamples.Rmd)
  Error: processing vignette 'GLMExamples.Rmd' failed with diagnostics:
  $ operator is invalid for atomic vectors
  --- failed re-building 'GLMExamples.Rmd'
  
  --- re-building 'UniModels.Rmd' using rmarkdown
  Loading required package: mcglm
  ----------------------------------------------------------------------
    mcglm: Multivariate Covariance Generalized Linear Models
  
    For support, collaboration or bug report, visit:
      http://mcglm.leg.ufpr.br/
  
    mcglm version 0.7.0 (build on 2021-07-07) is now loaded.
  ----------------------------------------------------------------------
  Loading required package: Matrix
  Loading required package: mvtnorm
  Loading required package: tweedie
  Quitting from lines 52-80 (UniModels.Rmd)
  Error: processing vignette 'UniModels.Rmd' failed with diagnostics:
  $ operator is invalid for atomic vectors
  --- failed re-building 'UniModels.Rmd'
  
  SUMMARY: processing the following files failed:
    'GLMExamples.Rmd' 'UniModels.Rmd'
  
  Error: Vignette re-building failed.
  Execution halted
  
• checking PDF version of manual ... OK
• DONE

Status: 4 ERRORs, 1 WARNING