• using R Under development (unstable) (2025-12-21 r89216)
• 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 ‘constellation/DESCRIPTION’ ... OK
• checking extension type ... Package
• this is package ‘constellation’ version ‘0.2.0’
• 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 ‘constellation’ can be installed ... OK See the install log for details.
• checking package directory ... OK
• checking for future file timestamps ... 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 code files for non-ASCII characters ... OK
• checking R files for syntax errors ... OK
• checking whether the package can be loaded ... [0s/0s] OK
• checking whether the package can be loaded with stated dependencies ... [0s/0s] OK
• checking whether the package can be unloaded cleanly ... [0s/1s] OK
• checking whether the namespace can be loaded with stated dependencies ... [0s/0s] OK
• checking whether the namespace can be unloaded cleanly ... [0s/1s] OK
• checking loading without being on the library search path ... [0s/1s] 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 ... [5s/7s] 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/1s] 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 ... [8s/4s] ERROR Running examples in ‘constellation-Ex.R’ failed The error most likely occurred in: > base::assign(".ptime", proc.time(), pos = "CheckExEnv") > ### Name: incidents > ### Title: Identify incident events separated by a minimum time window > ### Aliases: incidents > > ### ** Examples > > library(data.table) Attaching package: ‘data.table’ The following object is masked from ‘package:base’:     %notin% > systolic_bp <- as.data.table(vitals[VARIABLE == "SYSTOLIC_BP"]) > systolic_bp[, RECORDED_TIME := as.POSIXct(RECORDED_TIME, + format = "%Y-%m-%dT%H:%M:%SZ", tz = "UTC")] > > # Identify systolic blood pressure measurements for each patient that are > # separated by at least 24 hours > incidents(systolic_bp, window_hours = 24, join_key = "PAT_ID", + time_var = "RECORDED_TIME") Error in `[.data.table`(data, , `:=`(KEEP, get(time_var) >= (get(time_var)[1] + :   attempt access index 4/4 in VECTOR_ELT Calls: incidents -> [ -> [.data.table Execution halted
• checking for unstated dependencies in ‘tests’ ... OK
• checking tests ... [5s/6s] ERROR   Running ‘testthat.R’ [5s/6s] Running the tests in ‘tests/testthat.R’ failed. Complete output:   > library(testthat)   > library(constellation)   >   > test_check("constellation")   Saving _problems/test-incidents-47.R   [ FAIL 1 | WARN 0 | SKIP 0 | PASS 107 ]      ══ Failed tests ════════════════════════════════════════════════════════════════   ── Error ('test-incidents.R:45:3'): incidents produces expected values for test patient ──   Error in ``[.data.table`(data, , `:=`(KEEP, get(time_var) >= (get(time_var)[1] + window_hours * 60 * 60)), by = join_key)`: attempt access index 4/4 in VECTOR_ELT   Backtrace:       ▆    1. ├─testthat::expect_equal(...) at test-incidents.R:45:3    2. │ └─testthat::quasi_label(enquo(object), label)    3. │ └─rlang::eval_bare(expr, quo_get_env(quo))    4. └─constellation::incidents(...)    5. ├─...[]    6. └─data.table:::`[.data.table`(...)      [ FAIL 1 | WARN 0 | SKIP 0 | PASS 107 ]   Error:   ! Test failures.   Execution halted
• checking for unstated dependencies in vignettes ... OK
• checking package vignettes ... OK
• checking re-building of vignette outputs ... [3s/3s] ERROR Error(s) in re-building vignettes:   ... --- re-building ‘identify_sepsis.Rmd’ using rmarkdown Quitting from identify_sepsis.Rmd:169-173 [sepsis_incidents] ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ <error/rlang_error> Error in `[.data.table`: ! attempt access index 2/2 in VECTOR_ELT --- Backtrace:     ▆  1. └─constellation::incidents(...)  2. ├─...[]  3. └─data.table:::`[.data.table`(...) ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ Error: processing vignette 'identify_sepsis.Rmd' failed with diagnostics: attempt access index 2/2 in VECTOR_ELT --- failed re-building ‘identify_sepsis.Rmd’ SUMMARY: processing the following file failed:   ‘identify_sepsis.Rmd’ Error: Vignette re-building failed. Execution halted
• checking PDF version of manual ... [4s/6s] OK
• checking HTML version of manual ... [1s/1s] OK
• checking for non-standard things in the check directory ... OK
• DONE

Status: 3 ERRORs