Last updated on 2025-12-19 17:49:51 CET.
| Flavor | Version | Tinstall | Tcheck | Ttotal | Status | Flags |
|---|---|---|---|---|---|---|
| r-devel-linux-x86_64-debian-clang | 0.7.0 | 24.46 | 511.17 | 535.63 | OK | |
| r-devel-linux-x86_64-debian-gcc | 0.7.0 | 17.76 | 383.05 | 400.81 | OK | |
| r-devel-linux-x86_64-fedora-clang | 0.7.0 | 41.00 | OK | |||
| r-devel-linux-x86_64-fedora-gcc | 0.7.0 | 41.00 | 740.47 | 781.47 | ERROR | |
| r-devel-windows-x86_64 | 0.7.0 | 25.00 | 463.00 | 488.00 | OK | |
| r-patched-linux-x86_64 | 0.7.0 | 23.97 | 482.99 | 506.96 | OK | |
| r-release-linux-x86_64 | 0.7.0 | 23.76 | 484.15 | 507.91 | OK | |
| r-release-macos-arm64 | 0.7.0 | 9.00 | 122.00 | 131.00 | ERROR | |
| r-release-macos-x86_64 | 0.7.0 | 21.00 | 879.00 | 900.00 | OK | |
| r-release-windows-x86_64 | 0.7.0 | 27.00 | 465.00 | 492.00 | OK | |
| r-oldrel-macos-arm64 | 0.7.0 | 9.00 | 125.00 | 134.00 | ERROR | |
| r-oldrel-macos-x86_64 | 0.7.0 | 21.00 | 1009.00 | 1030.00 | OK | |
| r-oldrel-windows-x86_64 | 0.7.0 | 27.00 | 632.00 | 659.00 | OK |
Version: 0.7.0
Check: tests
Result: ERROR
Running ‘test-asserts.R’ [26s/29s]
Running ‘test-charlson.R’ [43s/77s]
Running ‘test-comorbidities.R’ [8s/15s]
Running ‘test-data-frame-tools.R’ [7s/12s]
Running ‘test-elixhauser-example.R’ [7s/11s]
Running ‘test-elixhauser.R’ [6s/12s]
Running ‘test-icd_compact_to_full.R’
Running ‘test-internal-data.R’ [35s/51s]
Running ‘test-is_icd.R’ [62s/116s]
Running ‘test-locked-bindings.R’ [14s/37s]
Running ‘test-longitudinal-comorbidities.R’ [9s/20s]
Running ‘test-longitudinal-pccc-v3.1.R’ [7s/11s]
Running ‘test-lookup_icd_codes.R’ [27s/53s]
Running ‘test-pccc-deltas.R’ [7s/22s]
Running ‘test-pccc.R’ [32s/66s]
Running ‘test-summary-charlson.R’ [12s/17s]
Running ‘test-summary-elixhauser.R’ [10s/13s]
Running ‘test-summary-pccc-subconditions.R’ [12s/13s]
Running ‘test-summary-pccc.R’ [17s/36s]
Running ‘test-tibble-datatable.R’ [19s/34s]
Running ‘test-vs-ahrq.R’ [11s/24s]
Running ‘test-vs-pccc_1.0.6.R’ [14s/27s]
Running ‘test-zero-row-inputs.R’ [9s/19s]
Running ‘utilities.R’
Running the tests in ‘tests/test-pccc-deltas.R’ failed.
Complete output:
> source('utilities.R')
> # test the construction and results of the icd to pccc mappings. the code to
> # build the data sets is in
> # inst/mappings/icd-codes-and-mappings.R
> #
> # ANY CHANGES IN THE CODES AND THESE TESTS MAY IMPACT THE WRITE UP AND THESE TESTS
> if (!requireNamespace("data.table", quietly = TRUE)) {
+ message("SKIP: data.table not available; skipping test-pccc-deltas.R")
+ quit(save = "no", status = 0, runLast = FALSE)
+ }
>
> #
> library(medicalcoder)
> library(data.table)
Attaching package: 'data.table'
The following object is masked from 'package:base':
%notin%
> setDTthreads(threads = 1L) # to prevent CPU time exceeding elapsed time on CRAN
>
> source(
+ system.file("mappings", "icd-codes-and-mappings.R", package = "medicalcoder"),
+ verbose = interactive()
+ )
Error in `[.data.table`(icd_codes, , `:=`(srcs, length(unique(src))), :
attempt access index 12/12 in VECTOR_ELT
Calls: source -> withVisible -> eval -> eval -> [ -> [.data.table
Execution halted
Flavor: r-devel-linux-x86_64-fedora-gcc
Version: 0.7.0
Check: re-building of vignette outputs
Result: ERROR
Error(s) in re-building vignettes:
--- re-building ‘charlson.Rmd’ using rmarkdown
[WARNING] Deprecated: --highlight-style. Use --syntax-highlighting instead.
--- finished re-building ‘charlson.Rmd’
--- re-building ‘comorbidities.Rmd’ using rmarkdown
[WARNING] Deprecated: --highlight-style. Use --syntax-highlighting instead.
--- finished re-building ‘comorbidities.Rmd’
--- re-building ‘elixhauser.Rmd’ using rmarkdown
[WARNING] Deprecated: --highlight-style. Use --syntax-highlighting instead.
--- finished re-building ‘elixhauser.Rmd’
--- re-building ‘icd.Rmd’ using rmarkdown
[WARNING] Deprecated: --highlight-style. Use --syntax-highlighting instead.
--- finished re-building ‘icd.Rmd’
--- re-building ‘pccc.Rmd’ using rmarkdown
Quitting from pccc.Rmd:836-853 [unnamed-chunk-18]
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
<error/rlang_error>
Error in `[.data.table`:
! attempt access index 3/3 in VECTOR_ELT
---
Backtrace:
▆
1. ├─...[]
2. └─data.table:::`[.data.table`(...)
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
Error: processing vignette 'pccc.Rmd' failed with diagnostics:
attempt access index 3/3 in VECTOR_ELT
--- failed re-building ‘pccc.Rmd’
SUMMARY: processing the following file failed:
‘pccc.Rmd’
Error: Vignette re-building failed.
Execution halted
Flavor: r-devel-linux-x86_64-fedora-gcc
Version: 0.7.0
Check: tests
Result: ERROR
Running ‘test-asserts.R’ [5s/5s]
Running ‘test-charlson.R’ [8s/8s]
Running ‘test-comorbidities.R’ [2s/2s]
Running ‘test-data-frame-tools.R’ [1s/1s]
Running ‘test-elixhauser-example.R’ [1s/1s]
Running ‘test-elixhauser.R’ [1s/1s]
Running ‘test-icd_compact_to_full.R’ [1s/1s]
Running ‘test-internal-data.R’ [7s/7s]
Running ‘test-is_icd.R’ [13s/13s]
Running ‘test-locked-bindings.R’ [2s/2s]
Running ‘test-longitudinal-comorbidities.R’ [2s/2s]
Running ‘test-longitudinal-pccc-v3.1.R’ [1s/1s]
Running ‘test-lookup_icd_codes.R’ [6s/6s]
Running the tests in ‘tests/test-lookup_icd_codes.R’ failed.
Complete output:
> source('utilities.R')
> library(medicalcoder)
>
> # lookup exact vs regex consistency
> lx <- lookup_icd_codes(c("E11.9","I50.9"), regex = FALSE)
> lf <- lookup_icd_codes(factor(c("E11.9","I50.9")), regex = FALSE)
> lr <- lookup_icd_codes(c("^E11\\.9$","^I50\\.9$"), regex = TRUE)
> stopifnot(
+ identical(lx, lf),
+ all(lx$full_code %in% lr$full_code),
+ all(lr$full_code %in% lx$full_code)
+ )
>
> # the following gives an error:
> # Error in merge.data.frame(x = input, y = matches, all.x = TRUE, by = c(ifelse(regex, :
> # negative length vectors are not allowed
> m <- tryCatchError(lookup_icd_codes(x = "", regex = TRUE))
*** caught segfault ***
address 0x690008000, cause 'invalid permissions'
Traceback:
1: merge.data.frame(x = input, y = matches, all.x = TRUE, by = col_order[1:2])
2: merge(x = input, y = matches, all.x = TRUE, by = col_order[1:2])
3: lookup_icd_codes(x = "", regex = TRUE)
4: doTryCatch(return(expr), name, parentenv, handler)
5: tryCatchOne(expr, names, parentenv, handlers[[1L]])
6: tryCatchList(expr, classes, parentenv, handlers)
7: tryCatch(expr, ..., error = function(e) { e})
8: tryCatchError(lookup_icd_codes(x = "", regex = TRUE))
An irrecoverable exception occurred. R is aborting now ...
Flavor: r-release-macos-arm64
Version: 0.7.0
Check: tests
Result: ERROR
Running ‘test-asserts.R’ [5s/5s]
Running ‘test-charlson.R’ [8s/8s]
Running ‘test-comorbidities.R’ [2s/2s]
Running ‘test-data-frame-tools.R’ [1s/1s]
Running ‘test-elixhauser-example.R’ [1s/1s]
Running ‘test-elixhauser.R’ [1s/1s]
Running ‘test-icd_compact_to_full.R’ [1s/1s]
Running ‘test-internal-data.R’ [7s/7s]
Running ‘test-is_icd.R’ [13s/13s]
Running ‘test-locked-bindings.R’ [2s/2s]
Running ‘test-longitudinal-comorbidities.R’ [2s/2s]
Running ‘test-longitudinal-pccc-v3.1.R’ [1s/1s]
Running ‘test-lookup_icd_codes.R’ [6s/6s]
Running the tests in ‘tests/test-lookup_icd_codes.R’ failed.
Complete output:
> source('utilities.R')
> library(medicalcoder)
>
> # lookup exact vs regex consistency
> lx <- lookup_icd_codes(c("E11.9","I50.9"), regex = FALSE)
> lf <- lookup_icd_codes(factor(c("E11.9","I50.9")), regex = FALSE)
> lr <- lookup_icd_codes(c("^E11\\.9$","^I50\\.9$"), regex = TRUE)
> stopifnot(
+ identical(lx, lf),
+ all(lx$full_code %in% lr$full_code),
+ all(lr$full_code %in% lx$full_code)
+ )
>
> # the following gives an error:
> # Error in merge.data.frame(x = input, y = matches, all.x = TRUE, by = c(ifelse(regex, :
> # negative length vectors are not allowed
> m <- tryCatchError(lookup_icd_codes(x = "", regex = TRUE))
*** caught segfault ***
address 0x680008000, cause 'invalid permissions'
Traceback:
1: merge.data.frame(x = input, y = matches, all.x = TRUE, by = col_order[1:2])
2: merge(x = input, y = matches, all.x = TRUE, by = col_order[1:2])
3: lookup_icd_codes(x = "", regex = TRUE)
4: doTryCatch(return(expr), name, parentenv, handler)
5: tryCatchOne(expr, names, parentenv, handlers[[1L]])
6: tryCatchList(expr, classes, parentenv, handlers)
7: tryCatch(expr, ..., error = function(e) { e})
8: tryCatchError(lookup_icd_codes(x = "", regex = TRUE))
An irrecoverable exception occurred. R is aborting now ...
Flavor: r-oldrel-macos-arm64