CRAN Package Check Results for Package surveillance

Last updated on 2021-02-27 02:48:38 CET.

Flavor Version Tinstall Tcheck Ttotal Status Flags
r-devel-linux-x86_64-debian-clang 1.19.0 74.84 539.21 614.05 WARN
r-devel-linux-x86_64-debian-gcc 1.19.0 57.03 406.60 463.63 NOTE
r-devel-linux-x86_64-fedora-clang 1.19.0 833.60 NOTE
r-devel-linux-x86_64-fedora-gcc 1.19.0 767.60 OK
r-devel-windows-ix86+x86_64 1.19.0 111.00 515.00 626.00 NOTE --no-vignettes
r-patched-linux-x86_64 1.19.0 65.28 518.20 583.48 NOTE
r-patched-solaris-x86 1.19.0 939.90 NOTE
r-release-linux-x86_64 1.19.0 65.35 519.43 584.78 NOTE
r-release-macos-x86_64 1.19.0 NOTE
r-release-windows-ix86+x86_64 1.19.0 140.00 638.00 778.00 NOTE --no-vignettes
r-oldrel-macos-x86_64 1.19.0 NOTE
r-oldrel-windows-ix86+x86_64 1.19.0 101.00 595.00 696.00 NOTE --no-vignettes

Check Details

Version: 1.19.0
Check: package dependencies
Result: NOTE
    Package suggested but not available for checking: 'INLA'
Flavors: r-devel-linux-x86_64-debian-clang, r-devel-linux-x86_64-debian-gcc, r-patched-linux-x86_64, r-patched-solaris-x86, r-release-linux-x86_64, r-release-macos-x86_64, r-oldrel-macos-x86_64

Version: 1.19.0
Check: re-building of vignette outputs
Result: WARN
    Error(s) in re-building vignettes:
     ...
    --- re-building 'glrnb.Rnw' using Sweave
    Loading required package: sp
    Loading required package: xtable
    This is surveillance 1.19.0. For overview type 'help(surveillance)'.
    glrnb: Fitting Poisson model because alpha == 0
    glrnb: Fitting Poisson model because alpha == 0
    glrnb: Fitting glm.nb model with alpha=0.225966923076071
    glrnb: Fitting glm.nb model with alpha=0.225966923076071
    glrnb: Fitting glm.nb model with alpha=0.225966923076071
    glrnb: Fitting glm.nb model with alpha=0.225966923076071
    glrnb: Fitting glm.nb model with alpha=0.225966923076071
    glrnb: Fitting glm.nb model with alpha=0.225966923076071
    glrnb: Fitting Poisson model because alpha == 0
    glrnb: Fitting Poisson model because alpha == 0
    glrnb: Fitting Poisson model because alpha == 0
    glrnb: Fitting Poisson model because alpha == 0
    glrnb: Fitting Poisson model because alpha == 0
    glrnb: Fitting Poisson model because alpha == 0
    glrnb: Fitting Poisson model because alpha == 0
    glrnb: Fitting Poisson model because alpha == 0
    glrnb: Fitting Poisson model because alpha == 0
    glrnb: Fitting Poisson model because alpha == 0
    glrnb: Fitting Poisson model because alpha == 0
    glrnb: Fitting Poisson model because alpha == 0
    glrnb: Fitting Poisson model because alpha == 0
    glrnb: Fitting Poisson model because alpha == 0
    glrnb: Fitting Poisson model because alpha == 0
    glrnb: Fitting Poisson model because alpha == 0
    glrnb: Fitting Poisson model because alpha == 0
    glrnb: Fitting Poisson model because alpha == 0
    --- finished re-building 'glrnb.Rnw'
    
    --- re-building 'hhh4.Rnw' using Sweave
    Loading required package: sp
    Loading required package: xtable
    This is surveillance 1.19.0. For overview type 'help(surveillance)'.
    Doing computations: FALSE
    --- finished re-building 'hhh4.Rnw'
    
    --- re-building 'monitoringCounts.Rnw' using Sweave
    Loading required package: sp
    Loading required package: xtable
    This is surveillance 1.19.0. For overview type 'help(surveillance)'.
    Loading required package: splines
    Loading required package: gamlss.data
    
    Attaching package: 'gamlss.data'
    
    The following object is masked from 'package:datasets':
    
     sleep
    
    Loading required package: gamlss.dist
    Loading required package: MASS
    Loading required package: nlme
    Loading required package: parallel
     ********** GAMLSS Version 5.2-0 **********
    For more on GAMLSS look at https://www.gamlss.com/
    Type gamlssNews() to see new features/changes/bug fixes.
    
    Warning in model.matrix.default(mt, mf, contrasts) :
     non-list contrasts argument ignored
    Warning in model.matrix.default(mt, mf, contrasts) :
     non-list contrasts argument ignored
    --- finished re-building 'monitoringCounts.Rnw'
    
    --- re-building 'surveillance.Rnw' using Sweave
    Loading required package: sp
    Loading required package: xtable
    This is surveillance 1.19.0. For overview type 'help(surveillance)'.
    Doing computations: FALSE
    --- finished re-building 'surveillance.Rnw'
    
    --- re-building 'hhh4_spacetime.Rnw' using knitr
    Loading required package: sp
    Loading required package: xtable
    This is surveillance 1.19.0. For overview type 'help(surveillance)'.
    Doing computations: FALSE
    Loading required namespace: spdep
    Note: range of maximum neighbour order by region is 3-5
    Loading required package: ggplot2
    Warning in library(package, lib.loc = lib.loc, character.only = TRUE, logical.return = TRUE, :
     there is no package called 'ggplot2'
    --- finished re-building 'hhh4_spacetime.Rnw'
    
    --- re-building 'twinSIR.Rnw' using knitr
    Loading required package: sp
    Loading required package: xtable
    This is surveillance 1.19.0. For overview type 'help(surveillance)'.
    Doing computations: FALSE
    Warning in `[.epidata`(x, 1:5, , drop = FALSE) :
     dropped class "epidata": subsetting blocks not allowed
    Initialized 1 log-baseline interval: 0.00 92.55
    Initial parameter vector: 1 1 1 1 0
    Computing OSAIC weights for 4 epidemic covariates based on 1000 simulations ...
    Initialized 1 log-baseline interval: 0.00 92.55
    Initial parameter vector: 1 1 1 1 1 1 0
    Computing OSAIC weights for 4 epidemic covariates based on 1000 simulations ...
    --- finished re-building 'twinSIR.Rnw'
    
    --- re-building 'twinstim.Rnw' using knitr
    Loading required package: sp
    Loading required package: xtable
    This is surveillance 1.19.0. For overview type 'help(surveillance)'.
    Doing computations: FALSE
    Loading required namespace: spdep
    Note: auto-generated neighbourhood matrix contains 1 island
    no epidemic component in model
    Setting up the model environment ...
    Loading required namespace: parallel
    'imdfit_powerlaw' was fit with disabled 'cumCIF' -> calculate it now ...
    Note: added the 'tau' component to object 'imdfit_powerlaw' for future use.
    Warning in knitr::write_bib(c("memoise", "sp", "rgdal", "polyclip", "maptools", :
     package(s) rgdal not found
    Warning in writeLines(enc2utf8(text), con, ..., useBytes = TRUE) :
     invalid char string in output conversion
    Error: processing vignette 'twinstim.Rnw' failed with diagnostics:
    Running 'texi2dvi' on 'twinstim.tex' failed.
    BibTeX errors:
    The top-level auxiliary file: twinstim.aux
    The style file: jss.bst
    Database file #1: references.bib
    Database file #2: twinstim-R.bib
    I was expecting a `,' or a `}'---line 25 of file twinstim-R.bib
     :
     : @Manual{R:polyclip,
    (Error may have been on previous line)
    I'm skipping whatever remains of this entry
    --- failed re-building 'twinstim.Rnw'
    
    SUMMARY: processing the following file failed:
     'twinstim.Rnw'
    
    Error: Vignette re-building failed.
    Execution halted
Flavor: r-devel-linux-x86_64-debian-clang

Version: 1.19.0
Check: installed package size
Result: NOTE
     installed size is 8.8Mb
     sub-directories of 1Mb or more:
     R 1.7Mb
     doc 2.4Mb
     libs 2.1Mb
Flavors: r-devel-linux-x86_64-fedora-clang, r-patched-solaris-x86, r-release-macos-x86_64, r-oldrel-macos-x86_64

Version: 1.19.0
Flags: --no-vignettes
Check: installed package size
Result: NOTE
     installed size is 8.8Mb
     sub-directories of 1Mb or more:
     R 1.7Mb
     doc 2.4Mb
     libs 2.2Mb
Flavors: r-devel-windows-ix86+x86_64, r-release-windows-ix86+x86_64, r-oldrel-windows-ix86+x86_64