* using log directory ‘/data/blackswan/ripley/R/packages/tests-devel/Rcan.Rcheck’ * using R Under development (unstable) (2025-12-20 r89211) * using platform: x86_64-pc-linux-gnu * R was compiled by gcc (GCC) 14.2.1 20240912 (Red Hat 14.2.1-3) GNU Fortran (GCC) 14.2.1 20240912 (Red Hat 14.2.1-3) * running under: Fedora Linux 40 (Workstation Edition) * using session charset: UTF-8 * checking for file ‘Rcan/DESCRIPTION’ ... OK * this is package ‘Rcan’ version ‘1.3.92’ * 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 ‘Rcan’ can be installed ... OK * checking package 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 code 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 whether startup messages can be suppressed ... 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/11s] 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 data for ASCII and uncompressed saves ... OK * checking examples ... ERROR Running examples in ‘Rcan-Ex.R’ failed The error most likely occurred in: > ### Name: ICD_group_CI5 > ### Title: ICD10 group detailed example > ### Aliases: ICD_group_CI5 > ### Keywords: datasets > > ### ** Examples > > > > data(ICD_group_CI5) > data(data_individual_file) > > #group individual data by > # 5 year age group > # ICd grouping from dataframe ICD_group_CI5 > > df_data_icd <- csu_group_cases(data_individual_file, + var_age="age", + group_by=c("sex", "regcode", "reglabel"), + df_ICD = ICD_group_CI5, + var_ICD ="site") Warning in csu_group_cases(data_individual_file, var_age = "age", group_by = c("sex", : Warning: 60 cases have age value > 150 and will be considered as unknown age Error in `[.data.table`(dt_data, , `:=`(group_id, .GRP), by = key(dt_data)) : attempt access index 8/8 in VECTOR_ELT Calls: csu_group_cases -> core.csu_group_cases -> [ -> [.data.table Execution halted * checking examples with --run-donttest ... ERROR Running examples in ‘Rcan-Ex.R’ failed The error most likely occurred in: > ### Name: ICD_group_CI5 > ### Title: ICD10 group detailed example > ### Aliases: ICD_group_CI5 > ### Keywords: datasets > > ### ** Examples > > > > data(ICD_group_CI5) > data(data_individual_file) > > #group individual data by > # 5 year age group > # ICd grouping from dataframe ICD_group_CI5 > > df_data_icd <- csu_group_cases(data_individual_file, + var_age="age", + group_by=c("sex", "regcode", "reglabel"), + df_ICD = ICD_group_CI5, + var_ICD ="site") Warning in csu_group_cases(data_individual_file, var_age = "age", group_by = c("sex", : Warning: 60 cases have age value > 150 and will be considered as unknown age Error in `[.data.table`(dt_data, , `:=`(group_id, .GRP), by = key(dt_data)) : attempt access index 8/8 in VECTOR_ELT Calls: csu_group_cases -> core.csu_group_cases -> [ -> [.data.table Execution halted * checking for unstated dependencies in ‘tests’ ... OK * checking tests ... Running ‘testthat.R’ ERROR Running the tests in ‘tests/testthat.R’ failed. Complete output: > > > library(testthat) > test_check("Rcan") Loading required package: Rcan Type example(Rcan) to see demo of the function. Saving _problems/test-Rcan-13.R Saving _problems/test-Rcan-34.R Population with less than 18 age group: registry_label nb_age_group India, Chennai (Madras) 16 South Australia 17 ASR have been computed for the age group 0-99+ Cumulative risk have been computed for the age group 0-74 ASR have been computed for the age group 0-99+ Saving _problems/test-Rcan-122.R Population with less than 18 age group: registry_label year nb_age_group Brazil, Goiania 1988 17 Brazil, Goiania 1989 17 Brazil, Goiania 1990 17 Brazil, Goiania 1991 17 Brazil, Goiania 1992 17 --- --- --- USA, Georgia, Atlanta: Black 2003 17 USA, Georgia, Atlanta: Black 2004 17 USA, Georgia, Atlanta: Black 2005 17 USA, Georgia, Atlanta: Black 2006 17 USA, Georgia, Atlanta: Black 2007 17 ASR have been computed for the age group 0-99+ Saving _problems/test-Rcan-149.R [ FAIL 4 | WARN 3 | SKIP 0 | PASS 3 ] ══ Failed tests ════════════════════════════════════════════════════════════════ ── Error ('test-Rcan.R:9:3'): Test csu_group_cases: 1 ────────────────────────── Error in ``[.data.table`(dt_data, , `:=`(group_id, .GRP), by = key(dt_data))`: attempt access index 8/8 in VECTOR_ELT Backtrace: ▆ 1. └─Rcan::csu_group_cases(...) at test-Rcan.R:9:3 2. └─Rcan:::core.csu_group_cases(...) 3. ├─dt_data[, `:=`(group_id, .GRP), by = key(dt_data)] 4. └─data.table:::`[.data.table`(...) ── Error ('test-Rcan.R:29:3'): Test csu_merge_cases_pop: 1 ───────────────────── Error in ``[.data.table`(dt_data, , `:=`(group_id, .GRP), by = key(dt_data))`: attempt access index 8/8 in VECTOR_ELT Backtrace: ▆ 1. └─Rcan::csu_group_cases(...) at test-Rcan.R:29:3 2. └─Rcan:::core.csu_group_cases(...) 3. ├─dt_data[, `:=`(group_id, .GRP), by = key(dt_data)] 4. └─data.table:::`[.data.table`(...) ── Error ('test-Rcan.R:120:3'): Test trend: 1 ────────────────────────────────── Error in ``[.data.table`(dt_data, , `:=`(CSU_smooth, loess(CSU_T ~ CSU_Y, span = smoothing)$fitted), by = CSU_BY)`: attempt access index 7/7 in VECTOR_ELT Backtrace: ▆ 1. └─Rcan::csu_time_trend(...) at test-Rcan.R:120:3 2. └─Rcan:::core.csu_time_trend(...) 3. ├─...[] 4. └─data.table:::`[.data.table`(...) ── Error ('test-Rcan.R:147:3'): Test eapc: 1 ─────────────────────────────────── Error in ``[.data.table`(dt_data, , `:=`(id_group, .GRP), by = group_by)`: attempt access index 8/8 in VECTOR_ELT Backtrace: ▆ 1. └─Rcan::csu_eapc(...) at test-Rcan.R:147:3 2. └─Rcan:::core.csu_eapc(...) 3. ├─dt_data[, `:=`(id_group, .GRP), by = group_by] 4. └─data.table:::`[.data.table`(...) [ FAIL 4 | WARN 3 | SKIP 0 | PASS 3 ] Error: ! Test failures. Execution halted * checking PDF version of manual ... OK * checking for non-standard things in the check directory ... OK * checking for detritus in the temp directory ... OK * checking for new files in some other directories ... OK * DONE Status: 3 ERRORs See ‘/data/blackswan/ripley/R/packages/tests-devel/Rcan.Rcheck/00check.log’ for details. Command exited with non-zero status 1 Time 1:18.65, 62.72 + 15.74