Last updated on 2026-02-11 07:51:16 CET.
| Package | ERROR | NOTE | OK |
|---|---|---|---|
| medicalcoder | 2 | 11 | |
| pedalfast.data | 13 | ||
| pedbp | 2 | 11 | |
| phoenix | 13 | ||
| pTITAN2 | 2 | 11 | |
| REDCapExporter | 2 | 11 |
Current CRAN status: ERROR: 2, OK: 11
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’ [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’ [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’ [6s/6s]
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
Current CRAN status: OK: 13
Current CRAN status: NOTE: 2, OK: 11
Version: 2.0.3
Check: installed package size
Result: NOTE
installed size is 5.7Mb
sub-directories of 1Mb or more:
libs 3.9Mb
Flavors: r-oldrel-macos-arm64, r-oldrel-macos-x86_64
Current CRAN status: OK: 13
Current CRAN status: NOTE: 2, OK: 11
Version: 1.0.2
Check: CRAN incoming feasibility
Result: NOTE
Maintainer: ‘Peter DeWitt <peter.dewitt@cuanschutz.edu>’
Package CITATION file contains call(s) to old-style citEntry(). Please
use bibentry() instead.
Flavors: r-devel-linux-x86_64-debian-clang, r-devel-linux-x86_64-debian-gcc
Current CRAN status: ERROR: 2, OK: 11
Version: 0.3.2
Check: tests
Result: ERROR
Running ‘test-as.data.frame.R’ [1s/1s]
Running ‘test-build_r_pkg.R’ [2s/2s]
Running ‘test-export.R’ [0s/3s]
Running ‘test-format_record.R’ [1s/1s]
Running ‘test-keyring.R’ [0s/0s]
Running the tests in ‘tests/test-export.R’ failed.
Complete output:
> library(REDCapExporter)
>
> # Tests rely on publicly available REDCap and tokens published
> # https://github.com/redcap-tools/redcap-test-datasets/tree/master
>
> # project_name token server_url pid server read_only operational notes
> # archer 9A81268476645C4E5F03428B8AC3AA7B https://bbmc.ouhsc.edu/redcap/api/ 153 oklahoma-bbmc TRUE TRUE simple structure; read-only
> # archer D70F9ACD1EDD6F151C6EA78683944E98 https://bbmc.ouhsc.edu/redcap/api/ 213 oklahoma-bbmc FALSE TRUE simple structure; read & write
> # archer 0434F0E9CF53ED0587847AB6E51DE762 https://bbmc.ouhsc.edu/redcap/api/ 212 oklahoma-bbmc TRUE TRUE longitudinal structure; read-only
> # archer D72C6485B52FE9F75D27B696977FBA43 https://bbmc.ouhsc.edu/redcap/api/ 268 oklahoma-bbmc TRUE TRUE Russian characters; read-only
>
> archer01_csv <-
+ tryCatch(
+ export_core(uri = 'https://bbmc.ouhsc.edu/redcap/api/', token = '9A81268476645C4E5F03428B8AC3AA7B'),
+ error = function(e) {e}
+ )
Getting Project Info
Getting project metadata
Getting user data
Getting project record
>
> Sys.setenv("REDCap_API_URI" = 'https://bbmc.ouhsc.edu/redcap/api/')
> Sys.setenv("REDCap_API_TOKEN" = '9A81268476645C4E5F03428B8AC3AA7B')
> archer01_json <- tryCatch(export_core(format = "json"), error = function(e) {e})
Getting Project Info
Getting project metadata
Getting user data
Getting project record
>
> if (inherits(archer01_csv, "error") | inherits(archer01_json, "error")) {
+ if (inherits(archer01_csv, "curl_error") | inherits(archer01_json, "curl_error")) {
+ # skip the rest of the testing
+ print(sprintf("Skip test-export.R after curl error: %s", archer01_csv$message))
+ } else {
+ stop("in test-export.R an non curl related error occured when initially calling export_core")
+ }
+ } else {
+
+ stopifnot(
+ inherits(archer01_csv, "rcer_rccore"),
+ inherits(archer01_json, "rcer_rccore"),
+ inherits(archer01_csv$project_raw, "rcer_raw_project"),
+ inherits(archer01_json$project_raw, "rcer_raw_project"),
+ inherits(archer01_csv$metadata_raw, "rcer_raw_metadata"),
+ inherits(archer01_json$metadata_raw, "rcer_raw_metadata"),
+ inherits(archer01_csv$project_raw, "rcer_raw_project"),
+ inherits(archer01_json$project_raw, "rcer_raw_project"),
+ inherits(archer01_csv$record_raw, "rcer_raw_record"),
+ inherits(archer01_json$record_raw, "rcer_raw_record"),
+ grepl("text/csv", attr(archer01_csv$record_raw, "Content-Type")),
+ grepl("application/json", attr(archer01_json$record_raw, "Content-Type"))
+ )
+
+ a1 <- format_record(archer01_csv)
+ a2 <- format_record(archer01_json)
+
+ # apparently the end of line characters are exported differently
+ a1$address <- gsub('\n', ' ', gsub('\r', '', a1$address))
+ a2$address <- gsub('\n', ' ', gsub('\r', '', a2$address))
+ a1$comments <- gsub('\n', ' ', gsub('\r', '', a1$comments))
+ a2$comments <- gsub('\n', ' ', gsub('\r', '', a2$comments))
+
+ stopifnot(isTRUE(all.equal(a1, a2)))
+
+ }
Error in `$<-.data.frame`(`*tmp*`, address, value = character(0)) :
replacement has 0 rows, data has 1
Calls: $<- -> $<-.data.frame
Execution halted
Flavor: r-devel-linux-x86_64-debian-gcc
Version: 0.3.2
Check: tests
Result: ERROR
Running ‘test-as.data.frame.R’
Running ‘test-build_r_pkg.R’
Running ‘test-export.R’
Running ‘test-format_record.R’
Running ‘test-keyring.R’
Running the tests in ‘tests/test-export.R’ failed.
Complete output:
> library(REDCapExporter)
>
> # Tests rely on publicly available REDCap and tokens published
> # https://github.com/redcap-tools/redcap-test-datasets/tree/master
>
> # project_name token server_url pid server read_only operational notes
> # archer 9A81268476645C4E5F03428B8AC3AA7B https://bbmc.ouhsc.edu/redcap/api/ 153 oklahoma-bbmc TRUE TRUE simple structure; read-only
> # archer D70F9ACD1EDD6F151C6EA78683944E98 https://bbmc.ouhsc.edu/redcap/api/ 213 oklahoma-bbmc FALSE TRUE simple structure; read & write
> # archer 0434F0E9CF53ED0587847AB6E51DE762 https://bbmc.ouhsc.edu/redcap/api/ 212 oklahoma-bbmc TRUE TRUE longitudinal structure; read-only
> # archer D72C6485B52FE9F75D27B696977FBA43 https://bbmc.ouhsc.edu/redcap/api/ 268 oklahoma-bbmc TRUE TRUE Russian characters; read-only
>
> archer01_csv <-
+ tryCatch(
+ export_core(uri = 'https://bbmc.ouhsc.edu/redcap/api/', token = '9A81268476645C4E5F03428B8AC3AA7B'),
+ error = function(e) {e}
+ )
Getting Project Info
Getting project metadata
Getting user data
Getting project record
>
> Sys.setenv("REDCap_API_URI" = 'https://bbmc.ouhsc.edu/redcap/api/')
> Sys.setenv("REDCap_API_TOKEN" = '9A81268476645C4E5F03428B8AC3AA7B')
> archer01_json <- tryCatch(export_core(format = "json"), error = function(e) {e})
Getting Project Info
Getting project metadata
Getting user data
Getting project record
>
> if (inherits(archer01_csv, "error") | inherits(archer01_json, "error")) {
+ if (inherits(archer01_csv, "curl_error") | inherits(archer01_json, "curl_error")) {
+ # skip the rest of the testing
+ print(sprintf("Skip test-export.R after curl error: %s", archer01_csv$message))
+ } else {
+ stop("in test-export.R an non curl related error occured when initially calling export_core")
+ }
+ } else {
+
+ stopifnot(
+ inherits(archer01_csv, "rcer_rccore"),
+ inherits(archer01_json, "rcer_rccore"),
+ inherits(archer01_csv$project_raw, "rcer_raw_project"),
+ inherits(archer01_json$project_raw, "rcer_raw_project"),
+ inherits(archer01_csv$metadata_raw, "rcer_raw_metadata"),
+ inherits(archer01_json$metadata_raw, "rcer_raw_metadata"),
+ inherits(archer01_csv$project_raw, "rcer_raw_project"),
+ inherits(archer01_json$project_raw, "rcer_raw_project"),
+ inherits(archer01_csv$record_raw, "rcer_raw_record"),
+ inherits(archer01_json$record_raw, "rcer_raw_record"),
+ grepl("text/csv", attr(archer01_csv$record_raw, "Content-Type")),
+ grepl("application/json", attr(archer01_json$record_raw, "Content-Type"))
+ )
+
+ a1 <- format_record(archer01_csv)
+ a2 <- format_record(archer01_json)
+
+ # apparently the end of line characters are exported differently
+ a1$address <- gsub('\n', ' ', gsub('\r', '', a1$address))
+ a2$address <- gsub('\n', ' ', gsub('\r', '', a2$address))
+ a1$comments <- gsub('\n', ' ', gsub('\r', '', a1$comments))
+ a2$comments <- gsub('\n', ' ', gsub('\r', '', a2$comments))
+
+ stopifnot(isTRUE(all.equal(a1, a2)))
+
+ }
Error in `$<-.data.frame`(`*tmp*`, address, value = character(0)) :
replacement has 0 rows, data has 1
Calls: $<- -> $<-.data.frame
Execution halted
Flavor: r-devel-linux-x86_64-fedora-gcc