* using log directory ‘/home/rstudio/webpages/epidemiology/cdc/usdata.Rcheck’ * using R version 3.5.1 (2018-07-02) * using platform: x86_64-pc-linux-gnu (64-bit) * using session charset: UTF-8 * using options ‘--no-manual --as-cran’ * checking for file ‘usdata/DESCRIPTION’ ... OK * checking extension type ... Package * this is package ‘usdata’ version ‘0.1.0’ * 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 ... ERROR Found the following non-portable file path: usdata/extdata/Conditions_contributing_to_deaths_involving_coronavirus_disease_2019__COVID-19___by_age_group_and_state__United_States.(1).csv Tarballs are only required to store paths of up to 100 bytes and cannot store those of more than 256 bytes, with restrictions including to 100 bytes for the final component. See section ‘Package structure’ in the ‘Writing R Extensions’ manual. OK * checking for sufficient/correct file permissions ... OK * checking serialization versions ... OK * checking whether package ‘usdata’ can be installed ... OK * checking installed package size ... OK * checking package directory ... OK * checking DESCRIPTION meta-information ... WARNING Non-standard license specification: What license is it under? Standardizable: FALSE * checking top-level files ... NOTE Non-standard file/directory found at top level: ‘extdata’ * 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 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 ... NOTE get_covid: no visible global function definition for ‘covid19’ get_covid: no visible global function definition for ‘%>%’ get_covid: no visible global function definition for ‘group_by’ get_covid: no visible binding for global variable ‘administrative_area_level_2’ get_covid: no visible global function definition for ‘arrange’ get_covid: no visible global function definition for ‘mutate’ get_covid: no visible binding for global variable ‘confirmed’ get_covid: no visible global function definition for ‘lag’ get_covid: no visible global function definition for ‘first’ get_covid: no visible binding for global variable ‘deaths’ get_covid: no visible binding for global variable ‘tests’ get_measures: no visible global function definition for ‘covid19’ get_measures: no visible global function definition for ‘%>%’ get_measures: no visible global function definition for ‘group_by’ get_measures: no visible binding for global variable ‘administrative_area_level_2’ get_measures: no visible global function definition for ‘summarise’ get_measures: no visible binding for global variable ‘retail_and_recreation_percent_change_from_baseline’ get_measures: no visible binding for global variable ‘transit_stations_percent_change_from_baseline’ get_measures: no visible binding for global variable ‘stringency_index’ get_measures: no visible binding for global variable ‘school_closing’ get_measures: no visible binding for global variable ‘gatherings_restrictions’ get_measures: no visible binding for global variable ‘population’ Undefined global functions or variables: %>% administrative_area_level_2 arrange confirmed covid19 deaths first gatherings_restrictions group_by lag mutate population retail_and_recreation_percent_change_from_baseline school_closing stringency_index summarise tests transit_stations_percent_change_from_baseline Consider adding importFrom("stats", "lag") to your NAMESPACE file. * checking Rd files ... OK * checking Rd metadata ... OK * checking Rd line widths ... OK * checking Rd cross-references ... OK * checking for missing documentation entries ... WARNING Undocumented code objects: ‘States_COVID19’ ‘acs’ ‘census’ ‘get_covid’ ‘get_measures’ ‘measures’ ‘us’ Undocumented data sets: ‘States_COVID19’ ‘acs’ ‘census’ ‘measures’ ‘us’ All user-level objects in a package should have documentation entries. See chapter ‘Writing R documentation files’ in the ‘Writing R Extensions’ manual. * 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 ... WARNING Warning: large data files saved inefficiently: size ASCII compress States_COVID19.rda 2.8Mb FALSE none measures.rda 566Kb FALSE none us.rda 564Kb FALSE none Note: significantly better compression could be obtained by using R CMD build --resave-data old_size new_size compress States_COVID19.rda 2.8Mb 204Kb xz census.rda 15Kb 11Kb xz measures.rda 566Kb 247Kb xz us.rda 564Kb 245Kb xz * checking examples ... OK * DONE Status: 1 ERROR, 3 WARNINGs, 2 NOTEs