CRAN Package Check Results for Package joineRmeta

Last updated on 2022-01-06 15:51:22 CET.

Flavor Version Tinstall Tcheck Ttotal Status Flags
r-devel-linux-x86_64-debian-clang 0.1.2 21.88 191.05 212.93 ERROR
r-devel-linux-x86_64-debian-gcc 0.1.2 17.90 140.36 158.26 ERROR
r-devel-linux-x86_64-fedora-clang 0.1.2 258.82 ERROR
r-devel-linux-x86_64-fedora-gcc 0.1.2 260.37 ERROR
r-devel-windows-x86_64-new-UL 0.1.2 90.00 205.00 295.00 ERROR
r-devel-windows-x86_64-new-TK 0.1.2 ERROR
r-patched-linux-x86_64 0.1.2 20.39 234.56 254.95 OK
r-release-linux-x86_64 0.1.2 21.62 232.94 254.56 OK
r-release-macos-arm64 0.1.2 OK
r-release-macos-x86_64 0.1.2 OK
r-release-windows-ix86+x86_64 0.1.2 44.00 265.00 309.00 OK
r-oldrel-macos-x86_64 0.1.2 OK
r-oldrel-windows-ix86+x86_64 0.1.2 45.00 267.00 312.00 OK

Check Details

Version: 0.1.2
Check: examples
Result: ERROR
    Running examples in 'joineRmeta-Ex.R' failed
    The error most likely occurred in:
    
    > base::assign(".ptime", proc.time(), pos = "CheckExEnv")
    > ### Name: fixef.jointmeta1
    > ### Title: Extract fixed effects
    > ### Aliases: fixef.jointmeta1
    >
    > ### ** Examples
    >
    > #change example data to jointdata object
    > jointdat2<-tojointdata(longitudinal = simdat2$longitudinal,
    + survival = simdat2$survival, id = 'id',longoutcome = 'Y',
    + timevarying = c('time','ltime'),
    + survtime = 'survtime', cens = 'cens',time = 'time')
    >
    > #set variables to factors
    > jointdat2$baseline$study <- as.factor(jointdat2$baseline$study)
    > jointdat2$baseline$treat <- as.factor(jointdat2$baseline$treat)
    >
    > #fit multi-study joint model
    > #note: for demonstration purposes only - max.it restricted to 2
    > #model would need more iterations to truely converge
    > onestagefit<-jointmeta1(data = jointdat2, long.formula = Y ~ 1 + time +
    + + treat + study, long.rand.ind = c('int'),
    + long.rand.stud = c('treat'),
    + sharingstrct = 'randprop',
    + surv.formula = Surv(survtime, cens) ~ treat,
    + study.name = 'study', strat = TRUE, max.it = 2)
    Running EM algorithm...
    Warning: Using formula(x) is deprecated when x is a character vector of length > 1.
     Consider formula(paste(x, collapse = " ")) instead.
    Warning: Using formula(x) is deprecated when x is a character vector of length > 1.
     Consider formula(paste(x, collapse = " ")) instead.
    [1] "Not converged"
    Calculating log-likelihood...
    Warning: Using formula(x) is deprecated when x is a character vector of length > 1.
     Consider formula(paste(x, collapse = " ")) instead.
    Warning: Using formula(x) is deprecated when x is a character vector of length > 1.
     Consider formula(paste(x, collapse = " ")) instead.
    
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    >
    > #extract longitudinal fixed effects
    > fixef(onestagefit, type = 'Longitudinal')
    Error in as.vector(fixef.long)[, 1] : incorrect number of dimensions
    Calls: fixef -> fixef.jointmeta1
    Execution halted
Flavors: r-devel-linux-x86_64-debian-clang, r-devel-linux-x86_64-debian-gcc

Version: 0.1.2
Check: re-building of vignette outputs
Result: WARN
    Error(s) in re-building vignettes:
     ...
    --- re-building 'joineRmeta.Rmd' using rmarkdown
    Loading 'meta' package (version 5.1-1).
    Type 'help(meta)' for a brief overview.
    Readers of 'Meta-Analysis with R (Use R!)' should install
    older version of 'meta' package: https://tinyurl.com/dt4y5drs
    Quitting from lines 569-570 (joineRmeta.Rmd)
    Error: processing vignette 'joineRmeta.Rmd' failed with diagnostics:
    incorrect number of dimensions
    --- failed re-building 'joineRmeta.Rmd'
    
    SUMMARY: processing the following file failed:
     'joineRmeta.Rmd'
    
    Error: Vignette re-building failed.
    Execution halted
Flavors: r-devel-linux-x86_64-debian-clang, r-devel-linux-x86_64-debian-gcc

Version: 0.1.2
Check: examples
Result: ERROR
    Running examples in ‘joineRmeta-Ex.R’ failed
    The error most likely occurred in:
    
    > ### Name: fixef.jointmeta1
    > ### Title: Extract fixed effects
    > ### Aliases: fixef.jointmeta1
    >
    > ### ** Examples
    >
    > #change example data to jointdata object
    > jointdat2<-tojointdata(longitudinal = simdat2$longitudinal,
    + survival = simdat2$survival, id = 'id',longoutcome = 'Y',
    + timevarying = c('time','ltime'),
    + survtime = 'survtime', cens = 'cens',time = 'time')
    >
    > #set variables to factors
    > jointdat2$baseline$study <- as.factor(jointdat2$baseline$study)
    > jointdat2$baseline$treat <- as.factor(jointdat2$baseline$treat)
    >
    > #fit multi-study joint model
    > #note: for demonstration purposes only - max.it restricted to 2
    > #model would need more iterations to truely converge
    > onestagefit<-jointmeta1(data = jointdat2, long.formula = Y ~ 1 + time +
    + + treat + study, long.rand.ind = c('int'),
    + long.rand.stud = c('treat'),
    + sharingstrct = 'randprop',
    + surv.formula = Surv(survtime, cens) ~ treat,
    + study.name = 'study', strat = TRUE, max.it = 2)
    Running EM algorithm...
    Warning: Using formula(x) is deprecated when x is a character vector of length > 1.
     Consider formula(paste(x, collapse = " ")) instead.
    Warning: Using formula(x) is deprecated when x is a character vector of length > 1.
     Consider formula(paste(x, collapse = " ")) instead.
    [1] "Not converged"
    Calculating log-likelihood...
    Warning: Using formula(x) is deprecated when x is a character vector of length > 1.
     Consider formula(paste(x, collapse = " ")) instead.
    Warning: Using formula(x) is deprecated when x is a character vector of length > 1.
     Consider formula(paste(x, collapse = " ")) instead.
    
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    >
    > #extract longitudinal fixed effects
    > fixef(onestagefit, type = 'Longitudinal')
    Error in as.vector(fixef.long)[, 1] : incorrect number of dimensions
    Calls: fixef -> fixef.jointmeta1
    Execution halted
Flavors: r-devel-linux-x86_64-fedora-clang, r-devel-linux-x86_64-fedora-gcc, r-devel-windows-x86_64-new-UL, r-devel-windows-x86_64-new-TK

Version: 0.1.2
Check: re-building of vignette outputs
Result: WARN
    Error(s) in re-building vignettes:
    --- re-building ‘joineRmeta.Rmd’ using rmarkdown
    Loading 'meta' package (version 5.1-1).
    Type 'help(meta)' for a brief overview.
    Readers of 'Meta-Analysis with R (Use R!)' should install
    older version of 'meta' package: https://tinyurl.com/dt4y5drs
    Quitting from lines 569-570 (joineRmeta.Rmd)
    Error: processing vignette 'joineRmeta.Rmd' failed with diagnostics:
    incorrect number of dimensions
    --- failed re-building ‘joineRmeta.Rmd’
    
    SUMMARY: processing the following file failed:
     ‘joineRmeta.Rmd’
    
    Error: Vignette re-building failed.
    Execution halted
Flavors: r-devel-linux-x86_64-fedora-clang, r-devel-linux-x86_64-fedora-gcc, r-devel-windows-x86_64-new-UL, r-devel-windows-x86_64-new-TK