Check results for 'epidm'

using R Under development (unstable) (2025-12-18 r89199)
using platform: x86_64-pc-linux-gnu
R was compiled by Debian clang version 21.1.7 (1) Debian flang version 21.1.7 (1)
running under: Debian GNU/Linux forky/sid
using session charset: UTF-8
checking for file ‘epidm/DESCRIPTION’ ... OK
this is package ‘epidm’ version ‘1.0.4’
package encoding: UTF-8
checking CRAN incoming feasibility ... [1s/2s] OK
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 serialization versions ... OK
checking whether package ‘epidm’ can be installed ... OK See the install log for details.
checking package directory ... OK
checking for future file timestamps ... 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 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 ... [1s/2s] OK
checking whether the package can be unloaded cleanly ... [1s/2s] OK
checking whether the namespace can be loaded with stated dependencies ... [1s/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 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 ... [11s/14s] OK
checking Rd files ... [0s/1s] 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 ... [0s/0s] OK
checking LazyData ... OK
checking data for ASCII and uncompressed saves ... OK
checking examples ... [2s/2s] ERROR Running examples in ‘epidm-Ex.R’ failed The error most likely occurred in: > base::assign(".ptime", proc.time(), pos = "CheckExEnv") > ### Name: cip_spells > ### Title: Continuous Inpatient (CIP) Spells > ### Aliases: cip_spells > > ### ** Examples > > > cip_test <- data.frame( + id = c('465','465','465','465','8418','8418','8418', + '8418','8418','8418','8418','8418','26443', + '26443','26443','33299','33299','33299','33299', + '33299','33299','33299','33299','33299','33299', + '52635','52635','52635','52635','52635','52635', + '52635','52635','52635','52635','52635','52635', + '52635','52635','52635','52635','52635','52635', + '52635','52635','52635','52635','52635','52635', + '52635','52635','52635','78915','78915','78915'), + provider = c('X1T','X1T','X1T','X1T','KHA','KHA','KHA', + 'KHA','KHA','KHA','KHA','KHA','BX2','BX2', + 'BX2','PXH','PXH','PXH','PXH','PXH','PXH', + 'PXH','PXH','PXH','PXH','9HA','9HA','9HA', + '9HA','9HA','9HA','9HA','9HA','9HA','9HA', + '9HA','9HA','9HA','9HA','9HA','9HA','YYT', + 'YYT','YYT','YYT','YYT','YYT','YYT','YYT', + 'YYT','YYT','YYT','ABX','ABX','ABX'), + spell_start = as.Date(c( + '2020-03-07','2020-03-07','2020-03-25','2020-04-03','2020-01-25', + '2020-01-26','2020-07-14','2020-08-02','2020-08-12','2020-08-19', + '2020-08-19','2020-11-19','2019-11-12','2020-04-17','2020-04-23', + '2020-07-03','2020-01-17','2020-02-07','2020-03-20','2020-04-27', + '2020-06-21','2020-07-02','2020-10-17','2020-11-27','2021-01-02', + '2019-12-31','2020-01-02','2020-01-14','2020-01-16','2020-02-07', + '2020-02-11','2020-02-14','2020-02-18','2020-02-21','2020-02-25', + '2020-02-28','2020-03-09','2020-03-11','2020-03-12','2020-03-13', + '2020-03-14','2020-02-04','2020-02-07','2020-02-11','2020-02-14', + '2020-02-18','2020-02-21','2020-02-25','2020-02-28','2020-03-09', + '2020-03-11','2020-03-12','2020-04-16','2020-04-24','2020-05-13')), + spell_end = as.Date(c( + '2020-03-07','2020-03-25','2020-04-02','2020-04-27','2020-01-25', + '2020-01-27','2020-07-17','2020-08-07','2020-08-14','2020-08-19', + '2020-08-22','2020-12-16','2020-04-17','2020-04-23','2020-05-20', + '2020-07-24','2020-01-28','2020-02-07','2020-03-23','2020-04-29', + '2020-06-21','2020-07-03','2020-11-27','2021-01-02','2021-01-10', + '2019-12-31','2020-01-11','2020-01-14','2020-02-04','2020-02-07', + '2020-02-11','2020-02-14','2020-02-18','2020-02-21','2020-02-25', + '2020-02-28','2020-03-09','2020-03-11','2020-03-12','2020-03-13', + '2020-03-30','2020-02-07','2020-02-11','2020-02-14','2020-02-18', + '2020-02-21','2020-02-25','2020-02-28','2020-03-09','2020-03-11', + '2020-03-12','2020-03-13','2020-04-24','2020-05-13','2020-06-11')), + adm_meth = c('21','81','21','81','21','21','11','21','21','21','21', + '21','21','81','21','81','21','21','21','21','21','21', + '21','13','13','12','22','12','2D','13','13','13','13', + '13','13','13','13','13','13','13','21','81','81','81', + '81','81','13','81','81','13','13','13','21','11','81'), + adm_src = c('19','51','19','51','19','51','19','51','19','19','19', + '51','19','51','19','51','19','19','19','19','19','19', + '19','51','19','19','19','19','19','19','19','19','19', + '19','19','19','51','51','51','51','19','51','51','51', + '51','51','51','51','51','51','51','51','19','51','51'), + dis_meth = c('1','1','1','1','1','1','1','1','1','1','1','4','1','1', + '4','1','1','1','1','1','1','1','8','1','4','1','1','1', + '1','1','1','1','1','1','1','1','1','1','1','1','1','1', + '1','1','1','1','1','1','1','1','1','1','1','1','2'), + dis_dest = c('51','51','51','54','51','19','19','19','19','51','19', + '79','51','51','79','65','19','19','19','19','19','29', + '98','51','79','19','19','19','51','19','19','19','51', + '51','51','19','19','51','51','19','51','51','51','51', + '51','51','51','51','51','51','51','51','29','54','19'), + patclass = c('1','1','1','1','1','1','1','1','1','1','1','1','1','1', + '1','1','1','1','1','1','1','1','1','1','1','2','1','2', + '1','2','2','2','2','2','2','2','2','2','2','2','1','1', + '1','1','1','1','1','1','1','1','1','1','1','1','1') + ) > > cip_spells(x=cip_test, + group_vars = c('id','provider'), + patient_classification = 'patclass', + spell_start_date = 'spell_start', + admission_method = 'adm_meth', + admission_source = 'adm_src', + spell_end_date = 'spell_end', + discharge_destination = 'dis_dest' + )[] Error in `[.data.table`(x, , `:=`(tmp.spellN, seq_len(.N)), by = group_vars) : attempt access index 9/9 in VECTOR_ELT Calls: cip_spells -> [ -> [.data.table Execution halted
checking PDF version of manual ... [5s/6s] OK
checking HTML version of manual ... [1s/2s] OK
checking for non-standard things in the check directory ... OK
DONE

Status: 1 ERROR