* using log directory ‘/srv/hornik/tmp/CRAN/SimInf.Rcheck’ * using R Under development (unstable) (2023-12-19 r85710) * using platform: x86_64-pc-linux-gnu * R was compiled by Debian clang version 17.0.6 (2) Debian flang-new version 17.0.6 (2) * running under: Debian GNU/Linux trixie/sid * using session charset: UTF-8 * checking for file ‘SimInf/DESCRIPTION’ ... OK * checking extension type ... Package * this is package ‘SimInf’ version ‘9.6.0’ * package encoding: UTF-8 * checking CRAN incoming feasibility ... [5s/6s] NOTE Maintainer: ‘Stefan Widgren ’ Found the following (possibly) invalid URLs: URL: https://CRAN.R-project.org/package=SimInf/vignettes/SimInf.pdf From: README.md Status: 200 Message: OK CRAN URL not in canonical form URL: https://app.codecov.io/gh/stewid/SimInf From: README.md Status: 200 Message: OK CRAN URL not in canonical form URL: https://doi.org/10.1098/rsif.2008.0172 From: NEWS.md Status: 200 Message: OK CRAN URL not in canonical form URL: https://doi.org/10.18637/jss.v091.i12 From: README.md Status: 200 Message: OK CRAN URL not in canonical form URL: https://github.com/stewid/SimInf From: DESCRIPTION README.md Status: 200 Message: OK CRAN URL not in canonical form URL: https://github.com/stewid/SimInf/actions/workflows/R-CI.yaml From: README.md Status: 200 Message: OK CRAN URL not in canonical form URL: https://github.com/stewid/SimInf/blob/main/LICENSE From: README.md Status: 200 Message: OK CRAN URL not in canonical form URL: https://github.com/stewid/SimInf/issues From: DESCRIPTION Status: 200 Message: OK CRAN URL not in canonical form URL: https://orcid.org/0000-0001-5745-2284 From: inst/doc/scheduled-events.html README.md Status: 200 Message: OK CRAN URL not in canonical form URL: https://orcid.org/0000-0002-3614-1732 From: README.md Status: 200 Message: OK CRAN URL not in canonical form URL: https://orcid.org/0000-0002-4291-712X From: README.md Status: 200 Message: OK CRAN URL not in canonical form URL: https://orcid.org/0000-0003-4328-7171 From: README.md Status: 200 Message: OK CRAN URL not in canonical form URL: https://semver.org/ From: README.md Status: 200 Message: OK CRAN URL not in canonical form Canonical CRAN.R-project.org URLs use https. Found the following (possibly) invalid ORCID iDs: iD: 0000-0001-5745-2284 (from: DESCRIPTION) iD: 0000-0002-3614-1732 (from: DESCRIPTION) iD: 0000-0002-4291-712X (from: DESCRIPTION) iD: 0000-0002-6576-9668 (from: DESCRIPTION) iD: 0000-0002-9678-9813 (from: DESCRIPTION) iD: 0000-0003-4328-7171 (from: DESCRIPTION) * checking package namespace information ... OK * checking package dependencies ... OK * 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 ‘SimInf’ can be installed ... [14s/14s] OK * used C compiler: ‘Debian clang version 17.0.6 (2)’ * checking package directory ... OK * checking for future file timestamps ... OK * checking ‘build’ directory ... 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 ... [1s/1s] OK * checking whether the package can be loaded with stated dependencies ... [1s/1s] OK * checking whether the package can be unloaded cleanly ... [1s/1s] OK * checking whether the namespace can be loaded with stated dependencies ... [1s/1s] OK * checking whether the namespace can be unloaded cleanly ... [1s/1s] OK * checking loading without being on the library search path ... [1s/1s] 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 ... [10s/10s] OK * checking Rd files ... [0s/0s] 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 ... [1s/1s] OK * checking LazyData ... OK * checking data for ASCII and uncompressed saves ... OK * checking line endings in shell scripts ... OK * checking line endings in C/C++/Fortran sources/headers ... OK * checking line endings in Makefiles ... OK * checking compilation flags in Makevars ... OK * checking for GNU extensions in Makefiles ... OK * checking for portable use of $(BLAS_LIBS) and $(LAPACK_LIBS) ... OK * checking use of PKG_*FLAGS in Makefiles ... OK * checking use of SHLIB_OPENMP_*FLAGS in Makefiles ... OK * checking pragmas in C/C++ headers and code ... OK * checking compilation flags used ... OK * checking compiled code ... OK * checking sizes of PDF files under ‘inst/doc’ ... OK * checking installed files from ‘inst/doc’ ... OK * checking files in ‘vignettes’ ... OK * checking examples ... [118s/15s] NOTE Examples with CPU (user + system) or elapsed time > 5s user system elapsed u0_SIR 11.736 0.814 1.712 u0_SISe3 11.905 0.360 0.828 u0_SIS 11.206 0.772 1.230 u0_SEIR 10.815 0.377 0.826 u0_SISe 8.329 0.276 0.928 nodes 7.191 0.494 0.656 plot 6.265 0.271 0.229 Examples with CPU time > 2.5 times elapsed time user system elapsed ratio run 1.570 0.030 0.055 29.091 pairs-SimInf_model-method 3.789 0.147 0.137 28.730 plot 6.265 0.271 0.229 28.541 punchcard-set 1.525 0.058 0.057 27.772 u0_SISe3 11.905 0.360 0.828 14.813 u0_SEIR 10.815 0.377 0.826 13.550 nodes 7.191 0.494 0.656 11.715 u0_SIS 11.206 0.772 1.230 9.738 u0_SISe 8.329 0.276 0.928 9.273 u0_SIR 11.736 0.814 1.712 7.331 * checking for unstated dependencies in ‘tests’ ... OK * checking tests ... [46s/39s] NOTE Running ‘SEIR.R’ [2s/2s] Running ‘SIR.R’ [3s/3s] Running ‘SIS.R’ [2s/2s] Running ‘SISe.R’ [1s/1s] Running ‘SISe3.R’ [1s/1s] Running ‘SISe3_sp.R’ [1s/1s] Running ‘SISe_sp.R’ [1s/1s] Running ‘SimInf.R’ [1s/1s] Running ‘SimInf_events.R’ [2s/2s] Running ‘SimInf_model.R’ [1s/1s] Running ‘abc-gdata.R’ [2s/2s] Running ‘abc-ldata.R’ [2s/2s] Running ‘abc.R’ [1s/1s] Running ‘density_ratio.R’ [1s/1s] Running ‘distributions.R’ [1s/1s] Running ‘edge_properties.R’ [1s/1s] Running ‘indiv_events.R’ [8s/1s] Running R code in ‘indiv_events.R’ had CPU time 6.3 times elapsed time Running ‘ldata_sp.R’ [1s/1s] Running ‘match_compartments.R’ [1s/1s] Running ‘measures.R’ [1s/1s] Running ‘mparse.R’ [2s/2s] Running ‘package_skeleton.R’ [1s/1s] Running ‘pfilter.R’ [1s/1s] Running ‘phi.R’ [1s/1s] Running ‘prevalence.R’ [1s/1s] Running ‘punchcard.R’ [1s/1s] Running ‘sample_select.R’ [1s/1s] Running ‘solver_aem.R’ [1s/1s] Running ‘u0.R’ [1s/1s] Running ‘v0.R’ [1s/1s] * checking for unstated dependencies in vignettes ... OK * checking package vignettes in ‘inst/doc’ ... OK * checking re-building of vignette outputs ... [17s/11s] OK * checking PDF version of manual ... [4s/4s] OK * checking HTML version of manual ... [2s/2s] OK * checking for non-standard things in the check directory ... OK * checking for detritus in the temp directory ... OK * DONE Status: 3 NOTEs