Last updated on 2020-04-11 09:49:57 CEST.
| Flavor | Version | Tinstall | Tcheck | Ttotal | Status | Flags |
|---|---|---|---|---|---|---|
| r-devel-linux-x86_64-debian-clang | 4.0.6 | 251.15 | 161.21 | 412.36 | ERROR | |
| r-devel-linux-x86_64-debian-gcc | 4.0.6 | 166.03 | 133.44 | 299.47 | ERROR | |
| r-devel-linux-x86_64-fedora-clang | 4.0.6 | 574.90 | ERROR | |||
| r-devel-linux-x86_64-fedora-gcc | 4.0.6 | 586.83 | ERROR | |||
| r-devel-windows-ix86+x86_64 | 4.0.6 | 459.00 | 348.00 | 807.00 | ERROR | |
| r-devel-windows-ix86+x86_64-gcc8 | 4.0.6 | 478.00 | 241.00 | 719.00 | ERROR | |
| r-patched-linux-x86_64 | 4.0.6 | 214.96 | 160.39 | 375.35 | ERROR | |
| r-patched-osx-x86_64 | 4.0.6 | ERROR | ||||
| r-patched-solaris-x86 | 4.0.6 | 536.00 | ERROR | |||
| r-release-linux-x86_64 | 4.0.6 | 207.24 | 149.75 | 356.99 | WARN | |
| r-release-windows-ix86+x86_64 | 4.0.6 | 474.00 | 290.00 | 764.00 | WARN | |
| r-release-osx-x86_64 | 4.0.6 | NOTE | ||||
| r-oldrel-windows-ix86+x86_64 | 4.0.6 | 621.00 | 307.00 | 928.00 | NOTE | |
| r-oldrel-osx-x86_64 | 4.0.6 | NOTE |
Version: 4.0.6
Check: whether package can be installed
Result: WARN
Found the following significant warnings:
'config' variable 'CPP' is deprecated
Flavors: r-devel-linux-x86_64-debian-clang, r-devel-linux-x86_64-debian-gcc, r-devel-linux-x86_64-fedora-clang, r-devel-linux-x86_64-fedora-gcc, r-patched-linux-x86_64, r-patched-osx-x86_64, r-patched-solaris-x86
Version: 4.0.6
Check: Rd \usage sections
Result: WARN
Documented arguments not in \usage in documentation object 'filter_valid':
'...'
Functions with \usage entries need to have the appropriate \alias
entries, and all their arguments documented.
The \usage entries must correspond to syntactically valid R code.
See chapter 'Writing R documentation files' in the 'Writing R
Extensions' manual.
Flavors: r-devel-linux-x86_64-debian-clang, r-devel-linux-x86_64-debian-gcc, r-devel-linux-x86_64-fedora-clang, r-devel-linux-x86_64-fedora-gcc, r-devel-windows-ix86+x86_64, r-devel-windows-ix86+x86_64-gcc8, r-patched-linux-x86_64, r-patched-osx-x86_64, r-patched-solaris-x86, r-release-linux-x86_64, r-release-windows-ix86+x86_64
Version: 4.0.6
Check: tests
Result: ERROR
Running 'testthat.R' [38s/41s]
Running the tests in 'tests/testthat.R' failed.
Complete output:
> # this is common code to all the tests, each of which runs test_check with a
> # different filter:
> library("icd")
> library("testthat", warn.conflicts = FALSE, quietly = TRUE)
> icd:::.show_options()
$icd.data.who_url
[1] "https://icd.who.int/browse10"
> # Definitely don't download data on CRAN
> if (!icd:::.env_var_is_true("NOT_CRAN")) {
+ old_offline <- options("icd.data.offline" = TRUE)
+ on.exit(options(old_offline), add = TRUE)
+ } else {
+ old_offline <- options("icd.data.offline" = FALSE)
+ on.exit(options(old_offline), add = TRUE)
+ }
> if (icd:::.env_var_is_true("ICD_TEST_SLOW")) {
+ old_test_slow <- options("icd.test_slow" = TRUE)
+ on.exit(options(old_test_slow), add = TRUE)
+ }
> old_interact <- options("icd.data.interact" = FALSE)
> on.exit(options(old_interact), add = TRUE)
> icd:::.show_options()
$icd.data.interact
[1] FALSE
$icd.data.offline
[1] TRUE
$icd.data.who_url
[1] "https://icd.who.int/browse10"
> testthat::test_check("icd")
loading helper-base.R
loading helper-icd10.R
-- 1. Failure: van_walraven comodbidity index and score (@test-score.R#333) ---
van_walraven(mydf, visit_name = "id", icd_name = "value", return_df = TRUE) not equivalent to data.frame(id = factor(c(1, 2, 3)), vanWalraven = c(10, 12, -2)).
Component "id": target is character, current is factor
== testthat results ===========================================================
[ OK: 6000 | SKIPPED: 35 | WARNINGS: 0 | FAILED: 1 ]
1. Failure: van_walraven comodbidity index and score (@test-score.R#333)
Error: testthat unit tests failed
Execution halted
Flavor: r-devel-linux-x86_64-debian-clang
Version: 4.0.6
Check: tests
Result: ERROR
Running ‘testthat.R’ [32s/46s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
> # this is common code to all the tests, each of which runs test_check with a
> # different filter:
> library("icd")
> library("testthat", warn.conflicts = FALSE, quietly = TRUE)
> icd:::.show_options()
$icd.data.who_url
[1] "https://icd.who.int/browse10"
> # Definitely don't download data on CRAN
> if (!icd:::.env_var_is_true("NOT_CRAN")) {
+ old_offline <- options("icd.data.offline" = TRUE)
+ on.exit(options(old_offline), add = TRUE)
+ } else {
+ old_offline <- options("icd.data.offline" = FALSE)
+ on.exit(options(old_offline), add = TRUE)
+ }
> if (icd:::.env_var_is_true("ICD_TEST_SLOW")) {
+ old_test_slow <- options("icd.test_slow" = TRUE)
+ on.exit(options(old_test_slow), add = TRUE)
+ }
> old_interact <- options("icd.data.interact" = FALSE)
> on.exit(options(old_interact), add = TRUE)
> icd:::.show_options()
$icd.data.interact
[1] FALSE
$icd.data.offline
[1] TRUE
$icd.data.who_url
[1] "https://icd.who.int/browse10"
> testthat::test_check("icd")
loading helper-base.R
loading helper-icd10.R
── 1. Failure: van_walraven comodbidity index and score (@test-score.R#333) ───
van_walraven(mydf, visit_name = "id", icd_name = "value", return_df = TRUE) not equivalent to data.frame(id = factor(c(1, 2, 3)), vanWalraven = c(10, 12, -2)).
Component "id": target is character, current is factor
══ testthat results ═══════════════════════════════════════════════════════════
[ OK: 6000 | SKIPPED: 35 | WARNINGS: 0 | FAILED: 1 ]
1. Failure: van_walraven comodbidity index and score (@test-score.R#333)
Error: testthat unit tests failed
Execution halted
Flavor: r-devel-linux-x86_64-debian-gcc
Version: 4.0.6
Check: installed package size
Result: NOTE
installed size is 13.2Mb
sub-directories of 1Mb or more:
R 1.8Mb
data 1.4Mb
libs 8.6Mb
Flavors: r-devel-linux-x86_64-fedora-clang, r-devel-windows-ix86+x86_64, r-devel-windows-ix86+x86_64-gcc8, r-patched-osx-x86_64, r-patched-solaris-x86, r-release-windows-ix86+x86_64, r-release-osx-x86_64, r-oldrel-windows-ix86+x86_64, r-oldrel-osx-x86_64
Version: 4.0.6
Check: data for non-ASCII characters
Result: NOTE
Note: found 20 marked UTF-8 strings
Flavors: r-devel-linux-x86_64-fedora-clang, r-devel-linux-x86_64-fedora-gcc, r-patched-osx-x86_64, r-patched-solaris-x86, r-release-osx-x86_64, r-oldrel-osx-x86_64
Version: 4.0.6
Check: tests
Result: ERROR
Running ‘testthat.R’ [45s/58s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
> # this is common code to all the tests, each of which runs test_check with a
> # different filter:
> library("icd")
> library("testthat", warn.conflicts = FALSE, quietly = TRUE)
> icd:::.show_options()
$icd.data.who_url
[1] "https://icd.who.int/browse10"
> # Definitely don't download data on CRAN
> if (!icd:::.env_var_is_true("NOT_CRAN")) {
+ old_offline <- options("icd.data.offline" = TRUE)
+ on.exit(options(old_offline), add = TRUE)
+ } else {
+ old_offline <- options("icd.data.offline" = FALSE)
+ on.exit(options(old_offline), add = TRUE)
+ }
> if (icd:::.env_var_is_true("ICD_TEST_SLOW")) {
+ old_test_slow <- options("icd.test_slow" = TRUE)
+ on.exit(options(old_test_slow), add = TRUE)
+ }
> old_interact <- options("icd.data.interact" = FALSE)
> on.exit(options(old_interact), add = TRUE)
> icd:::.show_options()
$icd.data.interact
[1] FALSE
$icd.data.offline
[1] TRUE
$icd.data.who_url
[1] "https://icd.who.int/browse10"
> testthat::test_check("icd")
loading helper-base.R
loading helper-icd10.R
── 1. Failure: van_walraven comodbidity index and score (@test-score.R#333) ───
van_walraven(mydf, visit_name = "id", icd_name = "value", return_df = TRUE) not equivalent to data.frame(id = factor(c(1, 2, 3)), vanWalraven = c(10, 12, -2)).
Component "id": target is character, current is factor
══ testthat results ═══════════════════════════════════════════════════════════
[ OK: 6000 | SKIPPED: 35 | WARNINGS: 0 | FAILED: 1 ]
1. Failure: van_walraven comodbidity index and score (@test-score.R#333)
Error: testthat unit tests failed
Execution halted
Flavor: r-devel-linux-x86_64-fedora-clang
Version: 4.0.6
Check: tests
Result: ERROR
Running ‘testthat.R’ [49s/159s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
> # this is common code to all the tests, each of which runs test_check with a
> # different filter:
> library("icd")
> library("testthat", warn.conflicts = FALSE, quietly = TRUE)
> icd:::.show_options()
$icd.data.who_url
[1] "https://icd.who.int/browse10"
> # Definitely don't download data on CRAN
> if (!icd:::.env_var_is_true("NOT_CRAN")) {
+ old_offline <- options("icd.data.offline" = TRUE)
+ on.exit(options(old_offline), add = TRUE)
+ } else {
+ old_offline <- options("icd.data.offline" = FALSE)
+ on.exit(options(old_offline), add = TRUE)
+ }
> if (icd:::.env_var_is_true("ICD_TEST_SLOW")) {
+ old_test_slow <- options("icd.test_slow" = TRUE)
+ on.exit(options(old_test_slow), add = TRUE)
+ }
> old_interact <- options("icd.data.interact" = FALSE)
> on.exit(options(old_interact), add = TRUE)
> icd:::.show_options()
$icd.data.interact
[1] FALSE
$icd.data.offline
[1] TRUE
$icd.data.who_url
[1] "https://icd.who.int/browse10"
> testthat::test_check("icd")
loading helper-base.R
loading helper-icd10.R
── 1. Failure: van_walraven comodbidity index and score (@test-score.R#333) ───
van_walraven(mydf, visit_name = "id", icd_name = "value", return_df = TRUE) not equivalent to data.frame(id = factor(c(1, 2, 3)), vanWalraven = c(10, 12, -2)).
Component "id": target is character, current is factor
══ testthat results ═══════════════════════════════════════════════════════════
[ OK: 6000 | SKIPPED: 35 | WARNINGS: 0 | FAILED: 1 ]
1. Failure: van_walraven comodbidity index and score (@test-score.R#333)
Error: testthat unit tests failed
Execution halted
Flavor: r-devel-linux-x86_64-fedora-gcc
Version: 4.0.6
Check: running tests for arch ‘i386’
Result: ERROR
Running 'testthat.R' [49s]
Running the tests in 'tests/testthat.R' failed.
Complete output:
> # this is common code to all the tests, each of which runs test_check with a
> # different filter:
> library("icd")
> library("testthat", warn.conflicts = FALSE, quietly = TRUE)
> icd:::.show_options()
$icd.data.who_url
[1] "https://icd.who.int/browse10"
> # Definitely don't download data on CRAN
> if (!icd:::.env_var_is_true("NOT_CRAN")) {
+ old_offline <- options("icd.data.offline" = TRUE)
+ on.exit(options(old_offline), add = TRUE)
+ } else {
+ old_offline <- options("icd.data.offline" = FALSE)
+ on.exit(options(old_offline), add = TRUE)
+ }
> if (icd:::.env_var_is_true("ICD_TEST_SLOW")) {
+ old_test_slow <- options("icd.test_slow" = TRUE)
+ on.exit(options(old_test_slow), add = TRUE)
+ }
> old_interact <- options("icd.data.interact" = FALSE)
> on.exit(options(old_interact), add = TRUE)
> icd:::.show_options()
$icd.data.interact
[1] FALSE
$icd.data.offline
[1] TRUE
$icd.data.who_url
[1] "https://icd.who.int/browse10"
> testthat::test_check("icd")
loading helper-base.R
loading helper-icd10.R
-- 1. Failure: van_walraven comodbidity index and score (@test-score.R#333) ---
van_walraven(mydf, visit_name = "id", icd_name = "value", return_df = TRUE) not equivalent to data.frame(id = factor(c(1, 2, 3)), vanWalraven = c(10, 12, -2)).
Component "id": target is character, current is factor
== testthat results ===========================================================
[ OK: 6000 | SKIPPED: 35 | WARNINGS: 0 | FAILED: 1 ]
1. Failure: van_walraven comodbidity index and score (@test-score.R#333)
Error: testthat unit tests failed
Execution halted
Flavor: r-devel-windows-ix86+x86_64
Version: 4.0.6
Check: running tests for arch ‘x64’
Result: ERROR
Running 'testthat.R' [49s]
Running the tests in 'tests/testthat.R' failed.
Complete output:
> # this is common code to all the tests, each of which runs test_check with a
> # different filter:
> library("icd")
> library("testthat", warn.conflicts = FALSE, quietly = TRUE)
> icd:::.show_options()
$icd.data.who_url
[1] "https://icd.who.int/browse10"
> # Definitely don't download data on CRAN
> if (!icd:::.env_var_is_true("NOT_CRAN")) {
+ old_offline <- options("icd.data.offline" = TRUE)
+ on.exit(options(old_offline), add = TRUE)
+ } else {
+ old_offline <- options("icd.data.offline" = FALSE)
+ on.exit(options(old_offline), add = TRUE)
+ }
> if (icd:::.env_var_is_true("ICD_TEST_SLOW")) {
+ old_test_slow <- options("icd.test_slow" = TRUE)
+ on.exit(options(old_test_slow), add = TRUE)
+ }
> old_interact <- options("icd.data.interact" = FALSE)
> on.exit(options(old_interact), add = TRUE)
> icd:::.show_options()
$icd.data.interact
[1] FALSE
$icd.data.offline
[1] TRUE
$icd.data.who_url
[1] "https://icd.who.int/browse10"
> testthat::test_check("icd")
loading helper-base.R
loading helper-icd10.R
-- 1. Failure: van_walraven comodbidity index and score (@test-score.R#333) ---
van_walraven(mydf, visit_name = "id", icd_name = "value", return_df = TRUE) not equivalent to data.frame(id = factor(c(1, 2, 3)), vanWalraven = c(10, 12, -2)).
Component "id": target is character, current is factor
== testthat results ===========================================================
[ OK: 6000 | SKIPPED: 35 | WARNINGS: 0 | FAILED: 1 ]
1. Failure: van_walraven comodbidity index and score (@test-score.R#333)
Error: testthat unit tests failed
Execution halted
Flavor: r-devel-windows-ix86+x86_64
Version: 4.0.6
Check: running tests for arch ‘i386’
Result: ERROR
Running 'testthat.R' [33s]
Running the tests in 'tests/testthat.R' failed.
Complete output:
> # this is common code to all the tests, each of which runs test_check with a
> # different filter:
> library("icd")
> library("testthat", warn.conflicts = FALSE, quietly = TRUE)
> icd:::.show_options()
$icd.data.who_url
[1] "https://icd.who.int/browse10"
> # Definitely don't download data on CRAN
> if (!icd:::.env_var_is_true("NOT_CRAN")) {
+ old_offline <- options("icd.data.offline" = TRUE)
+ on.exit(options(old_offline), add = TRUE)
+ } else {
+ old_offline <- options("icd.data.offline" = FALSE)
+ on.exit(options(old_offline), add = TRUE)
+ }
> if (icd:::.env_var_is_true("ICD_TEST_SLOW")) {
+ old_test_slow <- options("icd.test_slow" = TRUE)
+ on.exit(options(old_test_slow), add = TRUE)
+ }
> old_interact <- options("icd.data.interact" = FALSE)
> on.exit(options(old_interact), add = TRUE)
> icd:::.show_options()
$icd.data.interact
[1] FALSE
$icd.data.offline
[1] TRUE
$icd.data.who_url
[1] "https://icd.who.int/browse10"
> testthat::test_check("icd")
loading helper-base.R
loading helper-icd10.R
-- 1. Failure: van_walraven comodbidity index and score (@test-score.R#333) ---
van_walraven(mydf, visit_name = "id", icd_name = "value", return_df = TRUE) not equivalent to data.frame(id = factor(c(1, 2, 3)), vanWalraven = c(10, 12, -2)).
Component "id": target is character, current is factor
== testthat results ===========================================================
[ OK: 6000 | SKIPPED: 35 | WARNINGS: 0 | FAILED: 1 ]
1. Failure: van_walraven comodbidity index and score (@test-score.R#333)
Error: testthat unit tests failed
Execution halted
Flavor: r-devel-windows-ix86+x86_64-gcc8
Version: 4.0.6
Check: running tests for arch ‘x64’
Result: ERROR
Running 'testthat.R' [37s]
Running the tests in 'tests/testthat.R' failed.
Complete output:
> # this is common code to all the tests, each of which runs test_check with a
> # different filter:
> library("icd")
> library("testthat", warn.conflicts = FALSE, quietly = TRUE)
> icd:::.show_options()
$icd.data.who_url
[1] "https://icd.who.int/browse10"
> # Definitely don't download data on CRAN
> if (!icd:::.env_var_is_true("NOT_CRAN")) {
+ old_offline <- options("icd.data.offline" = TRUE)
+ on.exit(options(old_offline), add = TRUE)
+ } else {
+ old_offline <- options("icd.data.offline" = FALSE)
+ on.exit(options(old_offline), add = TRUE)
+ }
> if (icd:::.env_var_is_true("ICD_TEST_SLOW")) {
+ old_test_slow <- options("icd.test_slow" = TRUE)
+ on.exit(options(old_test_slow), add = TRUE)
+ }
> old_interact <- options("icd.data.interact" = FALSE)
> on.exit(options(old_interact), add = TRUE)
> icd:::.show_options()
$icd.data.interact
[1] FALSE
$icd.data.offline
[1] TRUE
$icd.data.who_url
[1] "https://icd.who.int/browse10"
> testthat::test_check("icd")
loading helper-base.R
loading helper-icd10.R
-- 1. Failure: van_walraven comodbidity index and score (@test-score.R#333) ---
van_walraven(mydf, visit_name = "id", icd_name = "value", return_df = TRUE) not equivalent to data.frame(id = factor(c(1, 2, 3)), vanWalraven = c(10, 12, -2)).
Component "id": target is character, current is factor
== testthat results ===========================================================
[ OK: 6000 | SKIPPED: 35 | WARNINGS: 0 | FAILED: 1 ]
1. Failure: van_walraven comodbidity index and score (@test-score.R#333)
Error: testthat unit tests failed
Execution halted
Flavor: r-devel-windows-ix86+x86_64-gcc8
Version: 4.0.6
Check: tests
Result: ERROR
Running ‘testthat.R’ [37s/41s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
> # this is common code to all the tests, each of which runs test_check with a
> # different filter:
> library("icd")
> library("testthat", warn.conflicts = FALSE, quietly = TRUE)
> icd:::.show_options()
$icd.data.who_url
[1] "https://icd.who.int/browse10"
> # Definitely don't download data on CRAN
> if (!icd:::.env_var_is_true("NOT_CRAN")) {
+ old_offline <- options("icd.data.offline" = TRUE)
+ on.exit(options(old_offline), add = TRUE)
+ } else {
+ old_offline <- options("icd.data.offline" = FALSE)
+ on.exit(options(old_offline), add = TRUE)
+ }
> if (icd:::.env_var_is_true("ICD_TEST_SLOW")) {
+ old_test_slow <- options("icd.test_slow" = TRUE)
+ on.exit(options(old_test_slow), add = TRUE)
+ }
> old_interact <- options("icd.data.interact" = FALSE)
> on.exit(options(old_interact), add = TRUE)
> icd:::.show_options()
$icd.data.interact
[1] FALSE
$icd.data.offline
[1] TRUE
$icd.data.who_url
[1] "https://icd.who.int/browse10"
> testthat::test_check("icd")
loading helper-base.R
loading helper-icd10.R
── 1. Failure: van_walraven comodbidity index and score (@test-score.R#333) ───
van_walraven(mydf, visit_name = "id", icd_name = "value", return_df = TRUE) not equivalent to data.frame(id = factor(c(1, 2, 3)), vanWalraven = c(10, 12, -2)).
Component "id": target is character, current is factor
══ testthat results ═══════════════════════════════════════════════════════════
[ OK: 6000 | SKIPPED: 35 | WARNINGS: 0 | FAILED: 1 ]
1. Failure: van_walraven comodbidity index and score (@test-score.R#333)
Error: testthat unit tests failed
Execution halted
Flavor: r-patched-linux-x86_64
Version: 4.0.6
Check: package dependencies
Result: NOTE
Package suggested but not available for checking: ‘RODBC’
Flavor: r-patched-osx-x86_64
Version: 4.0.6
Check: tests
Result: ERROR
Running ‘testthat.R’ [24s/32s]
Running the tests in ‘tests/testthat.R’ failed.
Last 13 lines of output:
[1] "https://icd.who.int/browse10"
> testthat::test_check("icd")
loading helper-base.R
loading helper-icd10.R
── 1. Failure: van_walraven comodbidity index and score (@test-score.R#333) ───
van_walraven(mydf, visit_name = "id", icd_name = "value", return_df = TRUE) not equivalent to data.frame(id = factor(c(1, 2, 3)), vanWalraven = c(10, 12, -2)).
Component "id": target is character, current is factor
══ testthat results ═══════════════════════════════════════════════════════════
[ OK: 6000 | SKIPPED: 35 | WARNINGS: 0 | FAILED: 1 ]
1. Failure: van_walraven comodbidity index and score (@test-score.R#333)
Error: testthat unit tests failed
Execution halted
Flavor: r-patched-osx-x86_64
Version: 4.0.6
Check: re-building of vignette outputs
Result: WARN
Error(s) in re-building vignettes:
--- re-building ‘CMS-HCC.Rmd’ using rmarkdown
dyld: lazy symbol binding failed: Symbol not found: ____chkstk_darwin
Referenced from: /usr/local/bin/pandoc (which was built for Mac OS X 10.15)
Expected in: /usr/lib/libSystem.B.dylib
dyld: Symbol not found: ____chkstk_darwin
Referenced from: /usr/local/bin/pandoc (which was built for Mac OS X 10.15)
Expected in: /usr/lib/libSystem.B.dylib
Error: processing vignette 'CMS-HCC.Rmd' failed with diagnostics:
pandoc document conversion failed with error 6
--- failed re-building ‘CMS-HCC.Rmd’
--- re-building ‘ICD-10.Rmd’ using rmarkdown
dyld: lazy symbol binding failed: Symbol not found: ____chkstk_darwin
Referenced from: /usr/local/bin/pandoc (which was built for Mac OS X 10.15)
Expected in: /usr/lib/libSystem.B.dylib
dyld: Symbol not found: ____chkstk_darwin
Referenced from: /usr/local/bin/pandoc (which was built for Mac OS X 10.15)
Expected in: /usr/lib/libSystem.B.dylib
Error: processing vignette 'ICD-10.Rmd' failed with diagnostics:
pandoc document conversion failed with error 6
--- failed re-building ‘ICD-10.Rmd’
--- re-building ‘PCCC.Rmd’ using rmarkdown
dyld: lazy symbol binding failed: Symbol not found: ____chkstk_darwin
Referenced from: /usr/local/bin/pandoc (which was built for Mac OS X 10.15)
Expected in: /usr/lib/libSystem.B.dylib
dyld: Symbol not found: ____chkstk_darwin
Referenced from: /usr/local/bin/pandoc (which was built for Mac OS X 10.15)
Expected in: /usr/lib/libSystem.B.dylib
Error: processing vignette 'PCCC.Rmd' failed with diagnostics:
pandoc document conversion failed with error 6
--- failed re-building ‘PCCC.Rmd’
--- re-building ‘charlson-scores.Rmd’ using rmarkdown
dyld: lazy symbol binding failed: Symbol not found: ____chkstk_darwin
Referenced from: /usr/local/bin/pandoc (which was built for Mac OS X 10.15)
Expected in: /usr/lib/libSystem.B.dylib
dyld: Symbol not found: ____chkstk_darwin
Referenced from: /usr/local/bin/pandoc (which was built for Mac OS X 10.15)
Expected in: /usr/lib/libSystem.B.dylib
Error: processing vignette 'charlson-scores.Rmd' failed with diagnostics:
pandoc document conversion failed with error 6
--- failed re-building ‘charlson-scores.Rmd’
--- re-building ‘compare-maps.Rmd’ using rmarkdown
dyld: lazy symbol binding failed: Symbol not found: ____chkstk_darwin
Referenced from: /usr/local/bin/pandoc (which was built for Mac OS X 10.15)
Expected in: /usr/lib/libSystem.B.dylib
dyld: Symbol not found: ____chkstk_darwin
Referenced from: /usr/local/bin/pandoc (which was built for Mac OS X 10.15)
Expected in: /usr/lib/libSystem.B.dylib
Error: processing vignette 'compare-maps.Rmd' failed with diagnostics:
pandoc document conversion failed with error 6
--- failed re-building ‘compare-maps.Rmd’
--- re-building ‘custom-maps.Rmd’ using rmarkdown
dyld: lazy symbol binding failed: Symbol not found: ____chkstk_darwin
Referenced from: /usr/local/bin/pandoc (which was built for Mac OS X 10.15)
Expected in: /usr/lib/libSystem.B.dylib
dyld: Symbol not found: ____chkstk_darwin
Referenced from: /usr/local/bin/pandoc (which was built for Mac OS X 10.15)
Expected in: /usr/lib/libSystem.B.dylib
Error: processing vignette 'custom-maps.Rmd' failed with diagnostics:
pandoc document conversion failed with error 6
--- failed re-building ‘custom-maps.Rmd’
--- re-building ‘introduction.Rmd’ using rmarkdown
dyld: lazy symbol binding failed: Symbol not found: ____chkstk_darwin
Referenced from: /usr/local/bin/pandoc (which was built for Mac OS X 10.15)
Expected in: /usr/lib/libSystem.B.dylib
dyld: Symbol not found: ____chkstk_darwin
Referenced from: /usr/local/bin/pandoc (which was built for Mac OS X 10.15)
Expected in: /usr/lib/libSystem.B.dylib
Error: processing vignette 'introduction.Rmd' failed with diagnostics:
pandoc document conversion failed with error 6
--- failed re-building ‘introduction.Rmd’
--- re-building ‘ranges.Rmd’ using rmarkdown
dyld: lazy symbol binding failed: Symbol not found: ____chkstk_darwin
Referenced from: /usr/local/bin/pandoc (which was built for Mac OS X 10.15)
Expected in: /usr/lib/libSystem.B.dylib
dyld: Symbol not found: ____chkstk_darwin
Referenced from: /usr/local/bin/pandoc (which was built for Mac OS X 10.15)
Expected in: /usr/lib/libSystem.B.dylib
Error: processing vignette 'ranges.Rmd' failed with diagnostics:
pandoc document conversion failed with error 6
--- failed re-building ‘ranges.Rmd’
--- re-building ‘country-lang-vers.Rnw’ using Sweave
--- finished re-building ‘country-lang-vers.Rnw’
--- re-building ‘efficiency.Rnw’ using Sweave
--- finished re-building ‘efficiency.Rnw’
SUMMARY: processing the following files failed:
‘CMS-HCC.Rmd’ ‘ICD-10.Rmd’ ‘PCCC.Rmd’ ‘charlson-scores.Rmd’
‘compare-maps.Rmd’ ‘custom-maps.Rmd’ ‘introduction.Rmd’ ‘ranges.Rmd’
Error: Vignette re-building failed.
Execution halted
Flavor: r-patched-osx-x86_64
Version: 4.0.6
Check: tests
Result: ERROR
Running ‘testthat.R’ [66s/77s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
> # this is common code to all the tests, each of which runs test_check with a
> # different filter:
> library("icd")
> library("testthat", warn.conflicts = FALSE, quietly = TRUE)
> icd:::.show_options()
$icd.data.who_url
[1] "https://icd.who.int/browse10"
> # Definitely don't download data on CRAN
> if (!icd:::.env_var_is_true("NOT_CRAN")) {
+ old_offline <- options("icd.data.offline" = TRUE)
+ on.exit(options(old_offline), add = TRUE)
+ } else {
+ old_offline <- options("icd.data.offline" = FALSE)
+ on.exit(options(old_offline), add = TRUE)
+ }
> if (icd:::.env_var_is_true("ICD_TEST_SLOW")) {
+ old_test_slow <- options("icd.test_slow" = TRUE)
+ on.exit(options(old_test_slow), add = TRUE)
+ }
> old_interact <- options("icd.data.interact" = FALSE)
> on.exit(options(old_interact), add = TRUE)
> icd:::.show_options()
$icd.data.interact
[1] FALSE
$icd.data.offline
[1] TRUE
$icd.data.who_url
[1] "https://icd.who.int/browse10"
> testthat::test_check("icd")
loading helper-base.R
loading helper-icd10.R
── 1. Failure: van_walraven comodbidity index and score (@test-score.R#333) ───
van_walraven(mydf, visit_name = "id", icd_name = "value", return_df = TRUE) not equivalent to data.frame(id = factor(c(1, 2, 3)), vanWalraven = c(10, 12, -2)).
Component "id": target is character, current is factor
══ testthat results ═══════════════════════════════════════════════════════════
[ OK: 6000 | SKIPPED: 35 | WARNINGS: 0 | FAILED: 1 ]
1. Failure: van_walraven comodbidity index and score (@test-score.R#333)
Error: testthat unit tests failed
Execution halted
Flavor: r-patched-solaris-x86