R Development Page

surveillance log file (check_x86_64_linux)

Tue Nov  5 13:45:40 2024: Checking package surveillance (SVN revision 3171) ...
Additional arguments to R CMD check: --no-examples --no-tests --no-vignettes
* using log directory ‘/srv/rf/building/build_2024-11-05-13-44/RF_PKG_CHECK/PKGS/surveillance.Rcheck’
* using R version 4.4.1 Patched (2024-08-05 r86980)
* using platform: x86_64-pc-linux-gnu
* R was compiled by
    gcc (Debian 12.2.0-14) 12.2.0
    GNU Fortran (Debian 12.2.0-14) 12.2.0
* running under: Debian GNU/Linux 12 (bookworm)
* 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 ‘1.24.1’
* checking CRAN incoming feasibility ... [15s/31s] NOTE
Maintainer: ‘Sebastian Meyer ’

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.
* 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 ... [23s/23s] OK
* used C compiler: ‘gcc (Debian 12.2.0-14) 12.2.0’
* used C++ compiler: ‘g++ (Debian 12.2.0-14) 12.2.0’
* checking installed package size ... OK
* checking package directory ... OK
* checking for future file timestamps ... NOTE
unable to verify current time
* 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 code files for non-ASCII characters ... OK
* checking R files for syntax errors ... OK
* checking whether the package can be loaded ... [2s/2s] OK
* checking whether the package can be loaded with stated dependencies ... [2s/2s] OK
* checking whether the package can be unloaded cleanly ... [2s/2s] OK
* checking whether the namespace can be loaded with stated dependencies ... [2s/2s] OK
* checking whether the namespace can be unloaded cleanly ... [2s/2s] OK
* checking loading without being on the library search path ... [2s/2s] OK
* checking whether startup messages can be suppressed ... [2s/2s] 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 ... [43s/43s] OK
* checking Rd files ... [3s/3s] 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 ... [2s/2s] 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':
  ‘figures/HMM.pdf’ ‘figures/fPeriods.R’ ‘figures/fPeriods2.pdf’
  ‘figures/fPeriods3.pdf’ ‘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/pMC.RData’
  ‘monitoringCounts-cache/pMarkovChain.RData’ ‘monitoringCounts.Rnw’
  ‘monitoringCounts.bib’ ‘references.bib’ ‘surveillance-cache.RData’
  ‘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 ... WARNING
Directory 'inst/doc' does not exist.
Package vignettes without corresponding single PDF/HTML:
  ‘glrnb.Rnw’
  ‘hhh4.Rnw’
  ‘surveillance.Rnw’
  ‘hhh4_spacetime.Rnw’
  ‘monitoringCounts.Rnw’
  ‘twinSIR.Rnw’
  ‘twinstim.Rnw’
* checking running R code from vignettes ... SKIPPED
* checking re-building of vignette outputs ... SKIPPED
* checking PDF version of manual ... [15s/15s] OK
* checking HTML version of manual ... [10s/9s] OK
* checking for non-standard things in the check directory ... OK
* checking for detritus in the temp directory ... OK
* DONE

Status: 2 WARNINGs, 3 NOTEs
See
  ‘/srv/rf/building/build_2024-11-05-13-44/RF_PKG_CHECK/PKGS/surveillance.Rcheck/00check.log’
for details.

Run time: 197.05 seconds.