Last updated on 2026-04-24 13:18:06 CEST.
| Flavor | Version | Tinstall | Tcheck | Ttotal | Status | Flags |
|---|---|---|---|---|---|---|
| r-devel-linux-x86_64-debian-clang | 0.1.0 | 3.10 | 254.93 | 258.03 | OK | |
| r-devel-linux-x86_64-debian-gcc | 0.1.0 | 2.19 | 186.14 | 188.33 | OK | |
| r-devel-linux-x86_64-fedora-clang | 0.1.0 | 5.00 | 427.11 | 432.11 | OK | |
| r-devel-linux-x86_64-fedora-gcc | 0.1.0 | 409.20 | OK | |||
| r-patched-linux-x86_64 | 0.1.0 | 3.44 | 239.87 | 243.31 | OK | |
| r-release-linux-x86_64 | 0.1.0 | 2.43 | 238.09 | 240.52 | OK | |
| r-release-macos-arm64 | 0.1.0 | OK | ||||
| r-release-macos-x86_64 | 0.1.0 | 2.00 | 65.00 | 67.00 | ERROR | |
| r-release-windows-x86_64 | 0.1.0 | 5.00 | 294.00 | 299.00 | OK | |
| r-oldrel-macos-arm64 | 0.1.0 | OK | ||||
| r-oldrel-macos-x86_64 | 0.1.0 | 2.00 | 201.00 | 203.00 | OK | |
| r-oldrel-windows-x86_64 | 0.1.0 | 6.00 | 296.00 | 302.00 | OK |
Version: 0.1.0
Check: examples
Result: ERROR
Running examples in ‘pminternal-Ex.R’ failed
The error most likely occurred in:
> ### Name: cal_plot
> ### Title: Plot apparent and bias-corrected calibration curves
> ### Aliases: cal_plot
>
> ### ** Examples
>
> library(pminternal)
> set.seed(456)
> # simulate data with two predictors that interact
> dat <- pmcalibration::sim_dat(N = 2000, a1 = -2, a3 = -.3)
> mean(dat$y)
[1] 0.1985
> dat$LP <- NULL # remove linear predictor
>
> # fit a (misspecified) logistic regression model
> m1 <- glm(y ~ x1 + x2, data=dat, family="binomial")
>
> # to get a plot of bias-corrected calibration we need
> # to specify 'eval' argument via 'calib_args'
> # this argument specifies at what points to evalulate the
> # calibration curve for plotting. The example below uses
> # 100 equally spaced points between the min and max
> # original prediction.
>
> p <- predict(m1, type="response")
> p100 <- seq(min(p), max(p), length.out=100)
>
> m1_iv <- validate(m1, method="cv_optimism", B=10,
+ calib_args = list(eval=p100))
Error in dyn.load(file, DLLpath = DLLpath, ...) :
unable to load shared object '/Volumes/Builds/packages/big-sur-x86_64/Rlib/4.6/data.table/libs/data_table.so':
dlopen(/Volumes/Builds/packages/big-sur-x86_64/Rlib/4.6/data.table/libs/data_table.so, 0x0006): Symbol not found: _IS_GROWABLE
Referenced from: <A2E3C2EA-FFF1-35E6-9621-C23F120F8433> /Volumes/Builds/packages/big-sur-x86_64/Rlib/4.6/data.table/libs/data_table.so
Expected in: <0A9590E7-21FF-3C2D-B0BD-160A5BF4B716> /Library/Frameworks/R.framework/Versions/4.6-x86_64/Resources/lib/libR.dylib
Calls: validate ... namespaceImport -> loadNamespace -> library.dynam -> dyn.load
Execution halted
Flavor: r-release-macos-x86_64
Version: 0.1.0
Check: re-building of vignette outputs
Result: ERROR
Error(s) in re-building vignettes:
--- re-building ‘missing-data.Rmd’ using rmarkdown
Quitting from missing-data.Rmd:21-48 [setup]
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
<error/rlang_error>
Error in `library()`:
! there is no package called 'mice'
---
Backtrace:
▆
1. └─base::library(mice)
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
Error: processing vignette 'missing-data.Rmd' failed with diagnostics:
there is no package called 'mice'
--- failed re-building ‘missing-data.Rmd’
--- re-building ‘pminternal.Rmd’ using rmarkdown
Quitting from pminternal.Rmd:31-49 [setup]
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
<error/rlang_error>
Error:
! package or namespace load failed for 'Hmisc' in dyn.load(file, DLLpath = DLLpath, ...):
unable to load shared object '/Volumes/Builds/packages/big-sur-x86_64/Rlib/4.6/data.table/libs/data_table.so':
dlopen(/Volumes/Builds/packages/big-sur-x86_64/Rlib/4.6/data.table/libs/data_table.so, 0x0006): Symbol not found: _IS_GROWABLE
Referenced from: <A2E3C2EA-FFF1-35E6-9621-C23F120F8433> /Volumes/Builds/packages/big-sur-x86_64/Rlib/4.6/data.table/libs/data_table.so
Expected in: <0A9590E7-21FF-3C2D-B0BD-160A5BF4B716> /Library/Frameworks/R.framework/Versions/4.6-x86_64/Resources/lib/libR.dylib
---
Backtrace:
▆
1. └─base::library(Hmisc)
2. └─base::tryCatch(...)
3. └─base (local) tryCatchList(expr, classes, parentenv, handlers)
4. └─base (local) tryCatchOne(expr, names, parentenv, handlers[[1L]])
5. └─value[[3L]](cond)
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
Error: processing vignette 'pminternal.Rmd' failed with diagnostics:
package or namespace load failed for 'Hmisc' in dyn.load(file, DLLpath = DLLpath, ...):
unable to load shared object '/Volumes/Builds/packages/big-sur-x86_64/Rlib/4.6/data.table/libs/data_table.so':
dlopen(/Volumes/Builds/packages/big-sur-x86_64/Rlib/4.6/data.table/libs/data_table.so, 0x0006): Symbol not found: _IS_GROWABLE
Referenced from: <A2E3C2EA-FFF1-35E6-9621-C23F120F8433> /Volumes/Builds/packages/big-sur-x86_64/Rlib/4.6/data.table/libs/data_table.so
Expected in: <0A9590E7-21FF-3C2D-B0BD-160A5BF4B716> /Library/Frameworks/R.framework/Versions/4.6-x86_64/Resources/lib/libR.dylib
--- failed re-building ‘pminternal.Rmd’
--- re-building ‘validate-examples.Rmd’ using rmarkdown
Quitting from validate-examples.Rmd:19-30 [setup]
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
<error/rlang_error>
Error:
! package or namespace load failed for 'Hmisc' in dyn.load(file, DLLpath = DLLpath, ...):
unable to load shared object '/Volumes/Builds/packages/big-sur-x86_64/Rlib/4.6/data.table/libs/data_table.so':
dlopen(/Volumes/Builds/packages/big-sur-x86_64/Rlib/4.6/data.table/libs/data_table.so, 0x0006): Symbol not found: _IS_GROWABLE
Referenced from: <A2E3C2EA-FFF1-35E6-9621-C23F120F8433> /Volumes/Builds/packages/big-sur-x86_64/Rlib/4.6/data.table/libs/data_table.so
Expected in: <0A9590E7-21FF-3C2D-B0BD-160A5BF4B716> /Library/Frameworks/R.framework/Versions/4.6-x86_64/Resources/lib/libR.dylib
---
Backtrace:
▆
1. └─base::library(Hmisc)
2. └─base::tryCatch(...)
3. └─base (local) tryCatchList(expr, classes, parentenv, handlers)
4. └─base (local) tryCatchOne(expr, names, parentenv, handlers[[1L]])
5. └─value[[3L]](cond)
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
Error: processing vignette 'validate-examples.Rmd' failed with diagnostics:
package or namespace load failed for 'Hmisc' in dyn.load(file, DLLpath = DLLpath, ...):
unable to load shared object '/Volumes/Builds/packages/big-sur-x86_64/Rlib/4.6/data.table/libs/data_table.so':
dlopen(/Volumes/Builds/packages/big-sur-x86_64/Rlib/4.6/data.table/libs/data_table.so, 0x0006): Symbol not found: _IS_GROWABLE
Referenced from: <A2E3C2EA-FFF1-35E6-9621-C23F120F8433> /Volumes/Builds/packages/big-sur-x86_64/Rlib/4.6/data.table/libs/data_table.so
Expected in: <0A9590E7-21FF-3C2D-B0BD-160A5BF4B716> /Library/Frameworks/R.framework/Versions/4.6-x86_64/Resources/lib/libR.dylib
--- failed re-building ‘validate-examples.Rmd’
SUMMARY: processing the following files failed:
‘missing-data.Rmd’ ‘pminternal.Rmd’ ‘validate-examples.Rmd’
Error: Vignette re-building failed.
Execution halted
Flavor: r-release-macos-x86_64