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surveillance log file (check_x86_64_linux)

Fri Aug  5 17:31:55 2022: Checking package surveillance (SVN revision 2874) ...
Additional arguments to R CMD check: --no-examples --no-tests --no-vignettes
* using log directory ‘/srv/rf/building/build_2022-08-05-17-30/RF_PKG_CHECK/PKGS/surveillance.Rcheck’
* using R version 4.2.1 Patched (2022-08-03 r82668)
* using platform: x86_64-pc-linux-gnu (64-bit)
* using session charset: UTF-8
* using options ‘--no-examples --no-tests --no-vignettes --as-cran’
* checking for file ‘surveillance/DESCRIPTION’ ... OK
* this is package ‘surveillance’ version ‘1.20.1’
* package encoding: latin1
* checking CRAN incoming feasibility ... WARNING
Maintainer: ‘Sebastian Meyer ’

Insufficient package version (submitted: 1.20.1, existing: 1.20.1)

Suggests or Enhances not in mainstream repositories:
  INLA
Availability using Additional_repositories specification:
  INLA   yes   https://inla.r-inla-download.org/R/stable/

Package has a VignetteBuilder field but no prebuilt vignette index.

Found the following (possibly) invalid URLs:
  URL: https://case.folkhalsomyndigheten.se/
    From: man/algo.outbreakP.Rd
    Status: Error
    Message: libcurl error code 28:
      	Failed to connect to case.folkhalsomyndigheten.se port 443: Connection timed out

Found the following (possibly) invalid DOIs:
  DOI: 10.1002/bimj.200900050
    From: DESCRIPTION
    Status: Service Unavailable
    Message: 503
  DOI: 10.1002/sim.4177
    From: DESCRIPTION
    Status: Service Unavailable
    Message: 503
  DOI: 10.1111/j.1541-0420.2011.01684.x
    From: DESCRIPTION
    Status: Service Unavailable
    Message: 503
* checking package namespace information ... OK
* checking package dependencies ... NOTE
Package suggested but not available for checking: ‘INLA’
* checking if this is a source package ... OK
* checking if there is a namespace ... OK
* checking for executable files ... OK
* checking for hidden files and directories ... OK
* checking for portable file names ... OK
* checking for sufficient/correct file permissions ... OK
* checking whether package ‘surveillance’ can be installed ... [31s/31s] OK
* checking installed package size ... NOTE
  installed size is  6.7Mb
  sub-directories of 1Mb or more:
    R      1.7Mb
    libs   2.5Mb
* checking package directory ... OK
* checking for future file timestamps ... 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
* 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 ... [44s/44s] OK
* checking Rd files ... [1s/1s] OK
* checking Rd metadata ... OK
* checking Rd line widths ... 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 data for ASCII and uncompressed saves ... OK
* checking R/sysdata.rda ... OK
* checking line endings in C/C++/Fortran sources/headers ... OK
* checking pragmas in C/C++ headers and code ... OK
* checking compilation flags used ... OK
* checking compiled code ... OK
* checking files in ‘vignettes’ ... WARNING
Files in the 'vignettes' directory but no files in 'inst/doc':
  ‘glrnb.Rnw’, ‘hhh4-cache.RData’, ‘hhh4.Rnw’,
    ‘hhh4_spacetime-cache.RData’, ‘hhh4_spacetime.Rnw’,
    ‘monitoringCounts-cache/boda.RData’,
    ‘monitoringCounts-cache/boda.covars.RData’,
    ‘monitoringCounts-cache/fPlot.R’,
    ‘monitoringCounts-cache/fPlot1.pdf’,
    ‘monitoringCounts-cache/fPlot2.pdf’,
    ‘monitoringCounts-cache/pMC.RData’,
    ‘monitoringCounts-cache/pMarkovChain.RData’,
    ‘monitoringCounts.Rnw’, ‘monitoringCounts.bib’, ‘references.bib’,
    ‘surveillance-cache.RData’, ‘surveillance-hmm.pdf’,
    ‘surveillance.Rnw’, ‘twinSIR-cache.RData’, ‘twinSIR.Rnw’,
    ‘twinstim-cache.RData’, ‘twinstim.Rnw’
* checking examples ... SKIPPED
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ... SKIPPED
* checking for unstated dependencies in vignettes ... OK
* checking package vignettes in ‘inst/doc’ ... WARNING
Directory 'inst/doc' does not exist.
Package vignettes without corresponding single PDF/HTML:
   ‘glrnb.Rnw’
   ‘hhh4.Rnw’
   ‘monitoringCounts.Rnw’
   ‘surveillance.Rnw’
   ‘hhh4_spacetime.Rnw’
   ‘twinSIR.Rnw’
   ‘twinstim.Rnw’

* checking running R code from vignettes ... SKIPPED
* checking re-building of vignette outputs ... SKIPPED
* checking PDF version of manual ... OK
* skipping checking HTML version of manual: no command ‘tidy’ found
* checking for non-standard things in the check directory ... OK
* checking for detritus in the temp directory ... OK
* DONE

Status: 3 WARNINGs, 2 NOTEs
See
  ‘/srv/rf/building/build_2022-08-05-17-30/RF_PKG_CHECK/PKGS/surveillance.Rcheck/00check.log’
for details.


Run time: 245.4 seconds.

Additional Logs:   00install.out
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