Check results for 'pminternal'

using R Under development (unstable) (2026-03-18 r89649)
using platform: x86_64-apple-darwin20
R was compiled by Apple clang version 14.0.0 (clang-1400.0.29.202) GNU Fortran (GCC) 14.2.0
running under: macOS Ventura 13.3.1
using session charset: UTF-8 * current time: 2026-04-01 21:00:24 UTC
checking for file ‘pminternal/DESCRIPTION’ ... OK
this is package ‘pminternal’ version ‘0.1.0’
package encoding: UTF-8
checking package namespace information ... OK
checking package dependencies ... INFO Package suggested but not available for checking: ‘mice’
checking if this is a source package ... OK
checking if there is a namespace ... OK
checking for executable files ... OK
checking for hidden files and directories ... OK
checking for portable file names ... OK
checking for sufficient/correct file permissions ... OK
checking whether package ‘pminternal’ can be installed ... [2s/3s] OK See the install log for details.
checking installed package size ... OK
checking package directory ... OK
checking ‘build’ directory ... OK
checking DESCRIPTION meta-information ... OK
checking top-level files ... OK
checking for left-over files ... OK
checking index information ... OK
checking package subdirectories ... OK
checking code files for non-ASCII characters ... OK
checking R files for syntax errors ... OK
checking whether the package can be loaded ... [0s/0s] OK
checking whether the package can be loaded with stated dependencies ... [0s/0s] OK
checking whether the package can be unloaded cleanly ... [0s/0s] OK
checking whether the namespace can be loaded with stated dependencies ... [0s/0s] OK
checking whether the namespace can be unloaded cleanly ... [0s/0s] OK
checking loading without being on the library search path ... [0s/0s] OK
checking dependencies in R code ... OK
checking S3 generic/method consistency ... OK
checking replacement functions ... OK
checking foreign function calls ... OK
checking R code for possible problems ... [3s/3s] OK
checking Rd files ... [0s/0s] OK
checking Rd metadata ... OK
checking Rd cross-references ... OK
checking for missing documentation entries ... OK
checking for code/documentation mismatches ... OK
checking Rd \usage sections ... OK
checking Rd contents ... OK
checking for unstated dependencies in examples ... OK
checking installed files from ‘inst/doc’ ... OK
checking files in ‘vignettes’ ... OK
checking examples ... [6s/9s] 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
checking for unstated dependencies in vignettes ... OK
checking package vignettes ... OK
checking re-building of vignette outputs ... [15s/21s] 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
checking PDF version of manual ... [7s/9s] OK
DONE Status: 2 ERRORs
using check arguments '--no-clean-on-error '