* using log directory ‘/data/gannet/ripley/R/packages/tests-MKL/oxcovid19.Rcheck’ * using R Under development (unstable) (2021-04-23 r80213) * using platform: x86_64-pc-linux-gnu (64-bit) * using session charset: UTF-8 * using option ‘--no-stop-on-test-error’ * checking for file ‘oxcovid19/DESCRIPTION’ ... OK * checking extension type ... Package * this is package ‘oxcovid19’ version ‘0.1.2’ * package encoding: UTF-8 * 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 ‘oxcovid19’ can be installed ... [12s/45s] OK * checking package directory ... 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 ... 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 ... [16s/62s] OK * checking Rd files ... 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 LazyData ... OK * checking data for ASCII and uncompressed saves ... OK * checking installed files from ‘inst/doc’ ... OK * checking files in ‘vignettes’ ... OK * checking examples ...Warning: elapsed-time limit of 30 minutes reached for sub-process [0m/30m] ERROR Running examples in ‘oxcovid19-Ex.R’ failed The error most likely occurred in: > ### Name: cite_sources > ### Title: Cite data sources > ### Aliases: cite_sources > > ### ** Examples > > epidata <- get_data_epidemiology(ccode = "UK", adm = 0) * checking for unstated dependencies in ‘tests’ ... OK * checking tests ... Running ‘spelling.R’ Running ‘testthat.R’Warning: elapsed-time limit of 1.5 hours reached for sub-process [0m/90m] [0m/90m] ERROR Running the tests in ‘tests/testthat.R’ failed. Complete output: > library(testthat) > library(oxcovid19) ___ ____ ___ __ __ ___ ____ _ ___ / _ \ __ __ / ___|/ _ \\ \ / /|_ _|| _ \ / | / _ \ | | | |\ \/ /| | | | | |\ \ / / | | | | | || || (_) | | |_| | > < | |___| |_| | \ V / | | | |_| || | \__, | \___/ /_/\_\ \____|\___/ \_/ |___||____/ |_| /_/ ___ _ _ | _ \ __ _ | |_ __ _ | |__ __ _ ___ ___ | | | | / _` || __|/ _` || '_ \ / _` |/ __| / _ \ | |_| || (_| || |_| (_| || |_) || (_| |\__ \| __/ |____/ \__,_| \__|\__,_||_.__/ \__,_||___/ \___| The OxCOVID19 Database makes use of several datasets. If you use any of the data provided by this package, please include the appropriate citation as described at the following website: https://covid19.eng.ox.ac.uk/data_sources.html > > test_check("oxcovid19") Warning messages: 1: In system(cmd, timeout = tlim) : command 'LANGUAGE=C R_TESTS=startup.Rs '/data/gannet/ripley/R/MKL/bin/R' CMD BATCH --vanilla 'testthat.R' 'testthat.Rout'' timed out after 5400s 2: elapsed-time limit of 1.5 hours reached for sub-process * checking for unstated dependencies in vignettes ... OK * checking package vignettes in ‘inst/doc’ ... OK * checking re-building of vignette outputs ...Warning: elapsed-time limit of 1.5 hours reached for sub-process [0m/90m] WARNING Error(s) in re-building vignettes: Warning: elapsed-time limit of 30 minutes reached for sub-process --- re-building ‘database_access.Rmd’ using rmarkdown ___ ____ ___ __ __ ___ ____ _ ___ / _ \ __ __ / ___|/ _ \\ \ / /|_ _|| _ \ / | / _ \ | | | |\ \/ /| | | | | |\ \ / / | | | | | || || (_) | | |_| | > < | |___| |_| | \ V / | | | |_| || | \__, | \___/ /_/\_\ \____|\___/ \_/ |___||____/ |_| /_/ ___ _ _ | _ \ __ _ | |_ __ _ | |__ __ _ ___ ___ | | | | / _` || __|/ _` || '_ \ / _` |/ __| / _ \ | |_| || (_| || |_| (_| || |_) || (_| |\__ \| __/ |____/ \__,_| \__|\__,_||_.__/ \__,_||___/ \___| The OxCOVID19 Database makes use of several datasets. If you use any of the data provided by this package, please include the appropriate citation as described at the following website: https://covid19.eng.ox.ac.uk/data_sources.html Attaching package: 'dplyr' The following objects are masked from 'package:stats': filter, lag The following objects are masked from 'package:base': intersect, setdiff, setequal, union Warning: elapsed-time limit of 30 minutes reached for sub-process --- re-building ‘oxcovid19.Rmd’ using rmarkdown --- re-building ‘visualisation_china.Rmd’ using rmarkdown ___ ____ ___ __ __ ___ ____ _ ___ / _ \ __ __ / ___|/ _ \\ \ / /|_ _|| _ \ / | / _ \ | | | |\ \/ /| | | | | |\ \ / / | | | | | || || (_) | | |_| | > < | |___| |_| | \ V / | | | |_| || | \__, | \___/ /_/\_\ \____|\___/ \_/ |___||____/ |_| /_/ ___ _ _ | _ \ __ _ | |_ __ _ | |__ __ _ ___ ___ | | | | / _` || __|/ _` || '_ \ / _` |/ __| / _ \ | |_| || (_| || |_| (_| || |_) || (_| |\__ \| __/ |____/ \__,_| \__|\__,_||_.__/ \__,_||___/ \___| The OxCOVID19 Database makes use of several datasets. If you use any of the data provided by this package, please include the appropriate citation as described at the following website: https://covid19.eng.ox.ac.uk/data_sources.html Attaching package: 'dplyr' The following objects are masked from 'package:stats': filter, lag The following objects are masked from 'package:base': intersect, setdiff, setequal, union * checking PDF version of manual ... OK * checking for non-standard things in the check directory ... OK * checking for detritus in the temp directory ... OK * DONE Status: 2 ERRORs, 1 WARNING See ‘/data/gannet/ripley/R/packages/tests-MKL/oxcovid19.Rcheck/00check.log’ for details. Command exited with non-zero status 1 Time 3:36:57, 91.92 + 9.15