* using log directory 'd:/Rcompile/CRANpkg/local/3.6/AMR.Rcheck' * using R version 3.6.3 (2020-02-29) * using platform: x86_64-w64-mingw32 (64-bit) * using session charset: ISO8859-1 * checking for file 'AMR/DESCRIPTION' ... OK * this is package 'AMR' version '1.6.0' * 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 hidden files and directories ... OK * checking for portable file names ... OK * checking whether package 'AMR' can be installed ... OK * checking installed package size ... NOTE installed size is 9.1Mb sub-directories of 1Mb or more: R 4.2Mb data 3.5Mb * 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 ... [43s] OK * checking Rd files ... OK * checking Rd metadata ... 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 installed files from 'inst/doc' ... OK * checking files in 'vignettes' ... OK * checking examples ... ERROR Running examples in 'AMR-Ex.R' failed The error most likely occurred in: > ### Name: as.rsi > ### Title: Interpret MIC and Disk Values, or Clean Raw R/SI Data > ### Aliases: as.rsi rsi is.rsi is.rsi.eligible as.rsi.mic as.rsi.disk > ### as.rsi.data.frame > > ### ** Examples > > summary(example_isolates) # see all R/SI results at a glance date hospital_id ward_icu ward_clinical Min. :2002-01-02 A:321 Mode :logical Mode :logical 1st Qu.:2005-07-31 B:663 FALSE:1354 FALSE:536 Median :2009-07-31 C:254 TRUE :646 TRUE :1464 Mean :2009-11-20 D:762 3rd Qu.:2014-05-30 Max. :2017-12-28 ward_outpatient age gender patient_id Mode :logical Min. :14.00 Length:2000 Length:2000 FALSE:1880 1st Qu.:63.00 Class :character Class :character TRUE :120 Median :74.00 Mode :character Mode :character Mean :71.06 3rd Qu.:82.00 Max. :97.00 mo PEN OXA Class :mo Class:rsi Class:rsi :0 %R :73.7% (n=1201) %R :31.2% (n=114) Unique:90 %SI :26.3% (n=428) %SI :68.8% (n=251) #1 :B_ESCHR_COLI - %S :25.6% (n=417) - %S :68.8% (n=251) #2 :B_STPHY_CONS - %I : 0.7% (n=11) - %I : 0.0% (n=0) #3 :B_STPHY_AURS FLC AMX AMC Class:rsi Class:rsi Class:rsi %R :29.5% (n=278) %R :59.6% (n=804) %R :23.7% (n=446) %SI :70.5% (n=665) %SI :40.4% (n=546) %SI :76.3% (n=1433) - %S :70.5% (n=665) - %S :40.2% (n=543) - %S :71.4% (n=1342) - %I : 0.0% (n=0) - %I : 0.2% (n=3) - %I : 4.8% (n=91) AMP TZP CZO Class:rsi Class:rsi Class:rsi %R :59.6% (n=804) %R :12.6% (n=126) %R :44.6% (n=199) %SI :40.4% (n=546) %SI :87.4% (n=875) %SI :55.4% (n=247) - %S :40.2% (n=543) - %S :86.1% (n=862) - %S :54.9% (n=245) - %I : 0.2% (n=3) - %I : 1.3% (n=13) - %I : 0.4% (n=2) FEP CXM FOX Class:rsi Class:rsi Class:rsi %R :14.2% (n=103) %R :26.3% (n=470) %R :27.4% (n=224) %SI :85.8% (n=621) %SI :73.7% (n=1319) %SI :72.6% (n=594) - %S :85.6% (n=620) - %S :72.5% (n=1297) - %S :71.6% (n=586) - %I : 0.1% (n=1) - %I : 1.2% (n=22) - %I : 1.0% (n=8) CTX CAZ CRO Class:rsi Class:rsi Class:rsi %R :15.5% (n=146) %R :66.5% (n=1204) %R :15.5% (n=146) %SI :84.5% (n=797) %SI :33.5% (n=607) %SI :84.5% (n=797) - %S :84.4% (n=796) - %S :33.5% (n=607) - %S :84.4% (n=796) - %I : 0.1% (n=1) - %I : 0.0% (n=0) - %I : 0.1% (n=1) GEN TOB AMK Class:rsi Class:rsi Class:rsi %R :24.6% (n=456) %R :34.4% (n=465) %R :63.7% (n=441) %SI :75.4% (n=1399) %SI :65.6% (n=886) %SI :36.3% (n=251) - %S :74.0% (n=1372) - %S :65.1% (n=879) - %S :36.3% (n=251) - %I : 1.5% (n=27) - %I : 0.5% (n=7) - %I : 0.0% (n=0) KAN TMP SXT Class:rsi Class:rsi Class:rsi %R :100.0% (n=471) %R :38.1% (n=571) %R :20.5% (n=361) %SI : 0.0% (n=0) %SI :61.9% (n=928) %SI :79.5% (n=1398) - %S : 0.0% (n=0) - %S :61.2% (n=918) - %S :79.1% (n=1392) - %I : 0.0% (n=0) - %I : 0.7% (n=10) - %I : 0.3% (n=6) NIT FOS LNZ Class:rsi Class:rsi Class:rsi %R :17.1% (n=127) %R :42.2% (n=148) %R :69.3% (n=709) %SI :82.9% (n=616) %SI :57.8% (n=203) %SI :30.7% (n=314) - %S :76.0% (n=565) - %S :57.8% (n=203) - %S :30.7% (n=314) - %I : 6.9% (n=51) - %I : 0.0% (n=0) - %I : 0.0% (n=0) CIP MFX VAN Class:rsi Class:rsi Class:rsi %R :16.2% (n=228) %R :33.6% (n=71) %R :38.3% (n=712) %SI :83.8% (n=1181) %SI :66.4% (n=140) %SI :61.7% (n=1149) - %S :78.9% (n=1112) - %S :64.5% (n=136) - %S :61.7% (n=1149) - %I : 4.9% (n=69) - %I : 1.9% (n=4) - %I : 0.0% (n=0) TEC TCY TGC Class:rsi Class:rsi Class:rsi %R :75.7% (n=739) %R :29.8% (n=357) %R :12.7% (n=101) %SI :24.3% (n=237) %SI :70.3% (n=843) %SI :87.3% (n=697) - %S :24.3% (n=237) - %S :68.3% (n=820) - %S :87.3% (n=697) - %I : 0.0% (n=0) - %I : 1.9% (n=23) - %I : 0.0% (n=0) DOX ERY CLI Class:rsi Class:rsi Class:rsi %R :27.7% (n=315) %R :57.2% (n=1084) %R :61.2% (n=930) %SI :72.3% (n=821) %SI :42.8% (n=810) %SI :38.8% (n=590) - %S :71.7% (n=814) - %S :42.3% (n=801) - %S :38.6% (n=586) - %I : 0.6% (n=7) - %I : 0.5% (n=9) - %I : 0.3% (n=4) AZM IPM MEM Class:rsi Class:rsi Class:rsi %R :57.2% (n=1084) %R : 6.2% (n=55) %R : 5.9% (n=49) %SI :42.8% (n=810) %SI :93.8% (n=834) %SI :94.1% (n=780) - %S :42.3% (n=801) - %S :92.7% (n=824) - %S :94.1% (n=780) - %I : 0.5% (n=9) - %I : 1.1% (n=10) - %I : 0.0% (n=0) MTR CHL COL Class:rsi Class:rsi Class:rsi %R :14.7% (n=5) %R :21.4% (n=33) %R :81.2% (n=1331) %SI :85.3% (n=29) %SI :78.6% (n=121) %SI :18.8% (n=309) - %S :85.3% (n=29) - %S :78.6% (n=121) - %S :18.8% (n=309) - %I : 0.0% (n=0) - %I : 0.0% (n=0) - %I : 0.0% (n=0) MUP RIF Class:rsi Class:rsi %R : 5.9% (n=16) %R :69.6% (n=698) %SI :94.1% (n=254) %SI :30.4% (n=305) - %S :93.0% (n=251) - %S :30.2% (n=303) - %I : 1.1% (n=3) - %I : 0.2% (n=2) > > if (require("skimr")) { + # class supported in skim() too: + skim(example_isolates) + } Loading required package: skimr Error: Problem with `summarise()` column `skimmed`. i `skimmed = purrr::map2(...)`. x Problem with `summarise()` input `..1`. i `..1 = dplyr::across(variable_names, mangled_skimmers$funs)`. x could not find function "pm_n_distinct" Backtrace: x 1. +-skimr::skim(example_isolates) 2. | +-dplyr::summarize(...) 3. | \-dplyr:::summarise.grouped_df(...) 4. | \-dplyr:::summarise_cols(.data, ..., caller_env = caller_env()) 5. | +-base::withCallingHandlers(...) 6. | \-mask$eval_all_summarise(quo) 7. +-purrr::map2(...) 8. | +-skimr:::.f(.x[[1L]], .y[[1L]], ...) 9. | \-skimr:::skim_by_type.data.frame(.x[[1L]], .y[[1L]], ...) 10. | +-dplyr::summarize(data, dplyr::across(variable_names, mangled_skimmers$funs)) 11. | \-dplyr:::summarise.data.frame(...) 12. | \-dplyr:::summarise_cols(.data, ..., caller_env = caller_env()) 13. | +-base::withCallingHandlers(...) 14. | \-mask$eval_all_summarise(quo) 15. +-base::.handleSimpleError(...) 16. | \-dplyr:::h(simpleError(msg, call)) 17. | \-rlang::abort(bullets, class = "dplyr_error") 18. | \-rlang:::signal_abort(cnd) 19. | \-base::signalCondition(cnd) 20. \-(function (e) ... Execution halted * checking for unstated dependencies in 'tests' ... OK * checking tests ... [4s] OK Running 'testthat.R' [4s] * checking for unstated dependencies in vignettes ... OK * checking package vignettes in 'inst/doc' ... OK * checking re-building of vignette outputs ... [62s] OK * checking PDF version of manual ... OK * DONE Status: 1 ERROR, 1 NOTE