Last updated on 2025-12-25 09:51:05 CET.
| Flavor | Version | Tinstall | Tcheck | Ttotal | Status | Flags |
|---|---|---|---|---|---|---|
| r-devel-linux-x86_64-debian-clang | 0.7.0 | 23.32 | 489.93 | 513.25 | ERROR | |
| r-devel-linux-x86_64-debian-gcc | 0.7.0 | 18.14 | 355.50 | 373.64 | ERROR | |
| r-devel-linux-x86_64-fedora-clang | 0.7.0 | 40.00 | 723.75 | 763.75 | OK | |
| r-devel-linux-x86_64-fedora-gcc | 0.7.0 | 40.00 | 801.36 | 841.36 | OK | |
| r-devel-windows-x86_64 | 0.7.0 | 25.00 | 463.00 | 488.00 | OK | |
| r-patched-linux-x86_64 | 0.7.0 | 25.11 | 478.84 | 503.95 | 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 | 26.00 | 463.00 | 489.00 | OK | |
| r-oldrel-macos-arm64 | 0.7.0 | 10.00 | 120.00 | 130.00 | ERROR | |
| r-oldrel-macos-x86_64 | 0.7.0 | 21.00 | 1009.00 | 1030.00 | OK | |
| r-oldrel-windows-x86_64 | 0.7.0 | 31.00 | 631.00 | 662.00 | OK |
Version: 0.7.0
Check: tests
Result: ERROR
Running ‘test-asserts.R’ [17s/22s]
Running ‘test-charlson.R’ [27s/33s]
Running ‘test-comorbidities.R’ [5s/6s]
Running ‘test-data-frame-tools.R’ [5s/6s]
Running ‘test-elixhauser-example.R’ [5s/6s]
Running ‘test-elixhauser.R’ [4s/6s]
Running ‘test-icd_compact_to_full.R’ [4s/5s]
Running ‘test-internal-data.R’ [22s/27s]
Running ‘test-is_icd.R’ [45s/59s]
Running ‘test-locked-bindings.R’ [8s/10s]
Running ‘test-longitudinal-comorbidities.R’ [6s/7s]
Running ‘test-longitudinal-pccc-v3.1.R’ [4s/5s]
Running ‘test-lookup_icd_codes.R’ [18s/22s]
Running ‘test-pccc-deltas.R’ [5s/7s]
Running ‘test-pccc.R’ [21s/26s]
Running ‘test-summary-charlson.R’ [7s/8s]
Running ‘test-summary-elixhauser.R’ [6s/7s]
Running ‘test-summary-pccc-subconditions.R’ [8s/10s]
Running ‘test-summary-pccc.R’ [11s/14s]
Running ‘test-tibble-datatable.R’ [19s/15s]
Running ‘test-vs-ahrq.R’ [7s/9s]
Running ‘test-vs-pccc_1.0.6.R’ [8s/10s]
Running ‘test-zero-row-inputs.R’ [6s/8s]
Running ‘utilities.R’ [0s/0s]
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-debian-clang
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
Flavors: r-devel-linux-x86_64-debian-clang, r-devel-linux-x86_64-debian-gcc
Version: 0.7.0
Check: tests
Result: ERROR
Running ‘test-asserts.R’ [12s/16s]
Running ‘test-charlson.R’ [18s/23s]
Running ‘test-comorbidities.R’ [4s/6s]
Running ‘test-data-frame-tools.R’ [4s/6s]
Running ‘test-elixhauser-example.R’ [4s/6s]
Running ‘test-elixhauser.R’ [3s/4s]
Running ‘test-icd_compact_to_full.R’ [3s/5s]
Running ‘test-internal-data.R’ [16s/21s]
Running ‘test-is_icd.R’ [28s/39s]
Running ‘test-locked-bindings.R’ [6s/8s]
Running ‘test-longitudinal-comorbidities.R’ [4s/6s]
Running ‘test-longitudinal-pccc-v3.1.R’ [5s/5s]
Running ‘test-lookup_icd_codes.R’ [13s/17s]
Running ‘test-pccc-deltas.R’ [4s/5s]
Running ‘test-pccc.R’ [15s/21s]
Running ‘test-summary-charlson.R’ [5s/7s]
Running ‘test-summary-elixhauser.R’ [5s/6s]
Running ‘test-summary-pccc-subconditions.R’ [5s/7s]
Running ‘test-summary-pccc.R’ [8s/10s]
Running ‘test-tibble-datatable.R’ [11s/12s]
Running ‘test-vs-ahrq.R’ [5s/6s]
Running ‘test-vs-pccc_1.0.6.R’ [8s/10s]
Running ‘test-zero-row-inputs.R’ [5s/7s]
Running ‘utilities.R’ [0s/0s]
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-debian-gcc
Version: 0.7.0
Check: tests
Result: ERROR
Running ‘test-asserts.R’ [5s/5s]
Running ‘test-charlson.R’ [7s/7s]
Running ‘test-comorbidities.R’ [1s/1s]
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’ [7s/7s]
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’ [6s/6s]
Running ‘test-is_icd.R’ [12s/12s]
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 0x6b0008000, 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
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