CRAN Package Check Results for Package surveillance

Last updated on 2021-01-19 14:47:17 CET.

Flavor Version Tinstall Tcheck Ttotal Status Flags
r-devel-linux-x86_64-debian-clang 1.18.0 73.54 578.15 651.69 NOTE
r-devel-linux-x86_64-debian-gcc 1.18.0 56.90 434.59 491.49 NOTE
r-devel-linux-x86_64-fedora-clang 1.18.0 856.06 NOTE
r-devel-linux-x86_64-fedora-gcc 1.18.0 795.00 OK
r-devel-windows-ix86+x86_64 1.18.0 109.00 543.00 652.00 NOTE --no-vignettes
r-patched-linux-x86_64 1.18.0 66.61 539.05 605.66 NOTE
r-patched-solaris-x86 1.18.0 982.00 NOTE
r-release-linux-x86_64 1.18.0 61.05 549.68 610.73 WARN
r-release-macos-x86_64 1.18.0 NOTE
r-release-windows-ix86+x86_64 1.18.0 124.00 565.00 689.00 NOTE --no-vignettes
r-oldrel-macos-x86_64 1.18.0 NOTE
r-oldrel-windows-ix86+x86_64 1.18.0 103.00 651.00 754.00 NOTE --no-vignettes

Check Details

Version: 1.18.0
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: 1.18.0
Check: installed package size
Result: NOTE
     installed size is 8.6Mb
     sub-directories of 1Mb or more:
     R 1.7Mb
     doc 2.2Mb
     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: 1.18.0
Check: Rd cross-references
Result: NOTE
    Undeclared packages ‘RColorBrewer’, ‘scoringRules’, ‘coin’, ‘gtable’ in Rd xrefs
Flavor: r-devel-linux-x86_64-fedora-clang

Version: 1.18.0
Flags: --no-vignettes
Check: installed package size
Result: NOTE
     installed size is 8.6Mb
     sub-directories of 1Mb or more:
     R 1.7Mb
     doc 2.2Mb
     libs 2.2Mb
Flavors: r-devel-windows-ix86+x86_64, r-release-windows-ix86+x86_64, r-oldrel-windows-ix86+x86_64

Version: 1.18.0
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 1.18.0. 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 1.18.0. 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 1.18.0. 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
    Error: processing vignette 'monitoringCounts.Rnw' failed with diagnostics:
    Running ‘texi2dvi’ on ‘monitoringCounts.tex’ failed.
    LaTeX errors:
    ! Undefined control sequence.
    \hyper@linkurl ...tionraw >>}\relax \Hy@colorlink
     \@urlcolor #1\Hy@xspace@en...
    l.80 \begin{document}
    
    ! Undefined control sequence.
    \close@pdflink ->\Hy@endcolorlink
     \Hy@VerboseLinkStop \pdfendlink
    l.80 \begin{document}
    
    --- failed re-building ‘monitoringCounts.Rnw’
    
    --- re-building ‘surveillance.Rnw’ using Sweave
    Loading required package: sp
    Loading required package: xtable
    This is surveillance 1.18.0. 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 1.18.0. For overview type 'help(surveillance)'.
    Doing computations: FALSE
    Loading required namespace: spdep
    Note: range of maximum neighbour order by region is 3-5
    Error: processing vignette 'hhh4_spacetime.Rnw' failed with diagnostics:
    Running ‘texi2dvi’ on ‘hhh4_spacetime.tex’ failed.
    LaTeX errors:
    ! Undefined control sequence.
    <recently read> \Hy@colorlink
    
    l.106 \begin{document}
    
    ! Undefined control sequence.
    \close@pdflink ->\Hy@endcolorlink
     \Hy@VerboseLinkStop \pdfendlink
    l.106 \begin{document}
    
    ! Undefined control sequence.
    <recently read> \Hy@colorlink
    
    l.106 \begin{document}
    
    ! Undefined control sequence.
    \close@pdflink ->\Hy@endcolorlink
     \Hy@VerboseLinkStop \pdfendlink
    l.106 \begin{document}
    
    ! Undefined control sequence.
    <recently read> \Hy@colorlink
    
    l.106 \begin{document}
    
    ! Undefined control sequence.
    \close@pdflink ->\Hy@endcolorlink
     \Hy@VerboseLinkStop \pdfendlink
    l.106 \begin{document}
    
    ! Undefined control sequence.
    <recently read> \Hy@colorlink
    
    l.106 \begin{document}
    
    ! Undefined control sequence.
    \close@pdflink ->\Hy@endcolorlink
     \Hy@VerboseLinkStop \pdfendlink
    l.106 \begin{document}
    
    ! Undefined control sequence.
    <recently read> \Hy@colorlink
    
    l.106 \begin{document}
    
    ! Undefined control sequence.
    \close@pdflink ->\Hy@endcolorlink
     \Hy@VerboseLinkStop \pdfendlink
    l.106 \begin{document}
    
    ! Undefined control sequence.
    \hyper@linkurl ...tionraw >>}\relax \Hy@colorlink
     \@urlcolor #1\Hy@xspace@en...
    l.106 \begin{document}
    
    ! Undefined control sequence.
    \close@pdflink ->\Hy@endcolorlink
     \Hy@VerboseLinkStop \pdfendlink
    l.106 \begin{document}
    
    --- failed re-building ‘hhh4_spacetime.Rnw’
    
    --- re-building ‘twinSIR.Rnw’ using knitr
    Loading required package: sp
    Loading required package: xtable
    This is surveillance 1.18.0. 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 ...
    Error: processing vignette 'twinSIR.Rnw' failed with diagnostics:
    Running ‘texi2dvi’ on ‘twinSIR.tex’ failed.
    LaTeX errors:
    ! Undefined control sequence.
    <recently read> \Hy@colorlink
    
    l.111 \begin{document}
    
    ! Undefined control sequence.
    \close@pdflink ->\Hy@endcolorlink
     \Hy@VerboseLinkStop \pdfendlink
    l.111 \begin{document}
    
    ! Undefined control sequence.
    <recently read> \Hy@colorlink
    
    l.111 \begin{document}
    
    ! Undefined control sequence.
    \close@pdflink ->\Hy@endcolorlink
     \Hy@VerboseLinkStop \pdfendlink
    l.111 \begin{document}
    
    ! Undefined control sequence.
    <recently read> \Hy@colorlink
    
    l.111 \begin{document}
    
    ! Undefined control sequence.
    \close@pdflink ->\Hy@endcolorlink
     \Hy@VerboseLinkStop \pdfendlink
    l.111 \begin{document}
    
    ! Undefined control sequence.
    <recently read> \Hy@colorlink
    
    l.111 \begin{document}
    
    ! Undefined control sequence.
    \close@pdflink ->\Hy@endcolorlink
     \Hy@VerboseLinkStop \pdfendlink
    l.111 \begin{document}
    
    ! Undefined control sequence.
    <recently read> \Hy@colorlink
    
    l.111 \begin{document}
    
    ! Undefined control sequence.
    \close@pdflink ->\Hy@endcolorlink
     \Hy@VerboseLinkStop \pdfendlink
    l.111 \begin{document}
    
    ! Undefined control sequence.
    \hyper@linkurl ...tionraw >>}\relax \Hy@colorlink
     \@urlcolor #1\Hy@xspace@en...
    l.111 \begin{document}
    
    ! Undefined control sequence.
    \close@pdflink ->\Hy@endcolorlink
     \Hy@VerboseLinkStop \pdfendlink
    l.111 \begin{document}
    
    --- failed re-building ‘twinSIR.Rnw’
    
    --- re-building ‘twinstim.Rnw’ using knitr
    Loading required package: sp
    Loading required package: xtable
    This is surveillance 1.18.0. 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
    Error: processing vignette 'twinstim.Rnw' failed with diagnostics:
    Running ‘texi2dvi’ on ‘twinstim.tex’ failed.
    LaTeX errors:
    ! Undefined control sequence.
    <recently read> \Hy@colorlink
    
    l.108 \begin{document}
    
    ! Undefined control sequence.
    \close@pdflink ->\Hy@endcolorlink
     \Hy@VerboseLinkStop \pdfendlink
    l.108 \begin{document}
    
    ! Undefined control sequence.
    <recently read> \Hy@colorlink
    
    l.108 \begin{document}
    
    ! Undefined control sequence.
    \close@pdflink ->\Hy@endcolorlink
     \Hy@VerboseLinkStop \pdfendlink
    l.108 \begin{document}
    
    ! Undefined control sequence.
    <recently read> \Hy@colorlink
    
    l.108 \begin{document}
    
    ! Undefined control sequence.
    \close@pdflink ->\Hy@endcolorlink
     \Hy@VerboseLinkStop \pdfendlink
    l.108 \begin{document}
    
    ! Undefined control sequence.
    <recently read> \Hy@colorlink
    
    l.108 \begin{document}
    
    ! Undefined control sequence.
    \close@pdflink ->\Hy@endcolorlink
     \Hy@VerboseLinkStop \pdfendlink
    l.108 \begin{document}
    
    ! Undefined control sequence.
    <recently read> \Hy@colorlink
    
    l.108 \begin{document}
    
    ! Undefined control sequence.
    \close@pdflink ->\Hy@endcolorlink
     \Hy@VerboseLinkStop \pdfendlink
    l.108 \begin{document}
    
    ! Undefined control sequence.
    <recently read> \Hy@colorlink
    
    l.108 \begin{document}
    
    ! Undefined control sequence.
    \close@pdflink ->\Hy@endcolorlink
     \Hy@VerboseLinkStop \pdfendlink
    l.108 \begin{document}
    
    ! Undefined control sequence.
    <recently read> \Hy@colorlink
    
    l.108 \begin{document}
    
    ! Undefined control sequence.
    \close@pdflink ->\Hy@endcolorlink
     \Hy@VerboseLinkStop \pdfendlink
    l.108 \begin{document}
    
    ! Undefined control sequence.
    \hyper@linkurl ...tionraw >>}\relax \Hy@colorlink
     \@urlcolor #1\Hy@xspace@en...
    l.108 \begin{document}
    
    ! Undefined control sequence.
    \close@pdflink ->\Hy@endcolorlink
     \Hy@VerboseLinkStop \pdfendlink
    l.108 \begin{document}
    
    --- failed re-building ‘twinstim.Rnw’
    
    SUMMARY: processing the following files failed:
     ‘monitoringCounts.Rnw’ ‘hhh4_spacetime.Rnw’ ‘twinSIR.Rnw’
     ‘twinstim.Rnw’
    
    Error: Vignette re-building failed.
    Execution halted
Flavor: r-release-linux-x86_64