* using log directory ‘/data/gannet/ripley/R/packages/tests-Suggests/doMIsaul.Rcheck’
* using R Under development (unstable) (2022-06-08 r82470)
* using platform: x86_64-pc-linux-gnu (64-bit)
* using session charset: UTF-8
* using option ‘--no-stop-on-test-error’
* checking for file ‘doMIsaul/DESCRIPTION’ ... OK
* this is package ‘doMIsaul’ version ‘1.0.1’
* package encoding: UTF-8
* checking package namespace information ... OK
* checking package dependencies ... NOTE
Package suggested but not available for checking: ‘CPE’
* 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 ‘doMIsaul’ can be installed ... [12s/12s] OK
* checking package 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 R files for non-ASCII characters ... OK
* checking R files for syntax errors ... OK
* checking whether the package can be loaded ... OK
* checking whether the package can be loaded with stated dependencies ... OK
* checking whether the package can be unloaded cleanly ... OK
* checking whether the namespace can be loaded with stated dependencies ... OK
* checking whether the namespace can be unloaded cleanly ... OK
* checking loading without being on the library search path ... OK
* checking use of S3 registration ... 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 ... [17s/17s] OK
* checking Rd files ... OK
* checking Rd metadata ... OK
* checking Rd line widths ... 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 examples ... ERROR
Running examples in ‘doMIsaul-Ex.R’ failed
The error most likely occurred in:

> ### Name: MImpute
> ### Title: Wrapper functions for multivariate imputation with survival data
> ###   or left-censored data
> ### Aliases: MImpute MImpute_surv MImpute_lcens MImpute_lcenssurv
> 
> ### ** Examples
> 
> data(cancer, package = "survival")
> cancer.imp <- MImpute(cancer[, -c(1:3)], 2)
> 
> ## MImpute_surv
> data(cancer, package = "survival")
> cancer$status <- cancer$status - 1
> cancer.imp <- MImpute_surv(cancer, 1)
> 
> ## MImpute_lcens
> toy <- iris[, 1:4]
> # censor on variables 3 and 4, with LOD at quantile .1 and .2.
> LODs <- toy[1, ]
> LODs[1, ] <-c(NA, NA, quantile(toy[,3], .2), quantile(toy[,4], .1))
> # Censor indicator
> Censored <- data.frame(Petal.Length = runif(150, 50,60),
+                        Petal.Width = runif(150, 50,60))
> Censored[toy[,3] < LODs[1, 3], 1] <- LODs[1, 3]
> Censored[toy[,4] < LODs[1, 4], 2] <- LODs[1, 4]
> # NA for censored data
> toy[toy[,3] < LODs[1, 3], 3] <- NA
> toy[toy[,4] < LODs[1, 4], 4] <- NA
> # Additional missing data
> toy[sample(1:nrow(toy), 30), 1] <- NA
> toy[sample(1:nrow(toy), 30), 3] <- NA
> toy[sample(1:nrow(toy), 30), 4] <- NA
> 
> toy.imp <- MImpute_lcens(data = toy, data.lod = Censored, standards = LODs,
+                          mi.m = 1, mice.log = FALSE)
Error in loadNamespace(x) : there is no package called ‘censReg’
Calls: MImpute_lcens ... loadNamespace -> withRestarts -> withOneRestart -> doWithOneRestart
Execution halted
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
  Running ‘testthat.R’ [18s/18s]
 [18s/18s] ERROR
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > library(testthat)
  > library(doMIsaul)
  > 
  > test_check("doMIsaul")
  Loading required namespace: mclust
  Failed with error:  'there is no package called 'mclust''
  Loading required namespace: CPE
  Failed with error:  'there is no package called 'CPE''
  Loading required namespace: mclust
  Failed with error:  'there is no package called 'mclust''
  [ FAIL 4 | WARN 0 | SKIP 3 | PASS 35 ]
  
  ══ Skipped tests ═══════════════════════════════════════════════════════════════
  • empty test (3)
  
  ══ Failed tests ════════════════════════════════════════════════════════════════
  ── Error (test-other.R:32:3): mi impute for censored ───────────────────────────
  <packageNotFoundError/error/condition>
  Error in `loadNamespace(x)`: there is no package called 'censReg'
  Backtrace:
       ▆
    1. ├─testthat::expect_equal(...) at test-other.R:32:2
    2. │ └─testthat::quasi_label(enquo(object), label, arg = "object")
    3. │   └─rlang::eval_bare(expr, quo_get_env(quo))
    4. ├─doMIsaul::MImpute_lcens(...)
    5. │ └─mice::mice(...)
    6. │   └─mice:::sampler(...)
    7. │     └─mice:::sampler.univ(...)
    8. │       ├─base::do.call(f, args = args)
    9. │       └─mice mice.impute.cens(...)
   10. │         └─doMIsaul doMI.cens.draw3(y = yy, ry = ryy, x = x, lod.j = lod.j)
   11. └─base::loadNamespace(x)
   12.   └─base::withRestarts(stop(cond), retry_loadNamespace = function() NULL)
   13.     └─base withOneRestart(expr, restarts[[1L]])
   14.       └─base doWithOneRestart(return(expr), restart)
  ── Error (test-output_tables.R:17:3): Output tables ────────────────────────────
  <packageNotFoundError/error/condition>
  Error in `loadNamespace(x)`: there is no package called 'reshape2'
  Backtrace:
       ▆
    1. ├─testthat::expect_equal(...) at test-output_tables.R:17:2
    2. │ └─testthat::quasi_label(enquo(object), label, arg = "object")
    3. │   └─rlang::eval_bare(expr, quo_get_env(quo))
    4. ├─base::nrow(...)
    5. ├─doMIsaul::table_categorical(...)
    6. │ ├─base::do.call(...)
    7. │ └─base::lapply(...)
    8. │   └─doMIsaul FUN(X[[i]], ...)
    9. └─base::loadNamespace(x)
   10.   └─base::withRestarts(stop(cond), retry_loadNamespace = function() NULL)
   11.     └─base withOneRestart(expr, restarts[[1L]])
   12.       └─base doWithOneRestart(return(expr), restart)
  ── Error (test-unsupMI.R:29:3): UnsupMI it self ────────────────────────────────
  <packageNotFoundError/error/condition>
  Error in `loadNamespace(x)`: there is no package called 'censReg'
  Backtrace:
       ▆
    1. ├─testthat::expect_equal(...) at test-unsupMI.R:29:2
    2. │ └─testthat::quasi_label(enquo(object), label, arg = "object")
    3. │   └─rlang::eval_bare(expr, quo_get_env(quo))
    4. ├─doMIsaul::unsupMI(...)
    5. │ └─doMIsaul::MImpute_lcens(...)
    6. │   └─mice::mice(...)
    7. │     └─mice:::sampler(...)
    8. │       └─mice:::sampler.univ(...)
    9. │         ├─base::do.call(f, args = args)
   10. │         └─mice mice.impute.cens(...)
   11. │           └─doMIsaul doMI.cens.draw3(y = yy, ry = ryy, x = x, lod.j = lod.j)
   12. └─base::loadNamespace(x)
   13.   └─base::withRestarts(stop(cond), retry_loadNamespace = function() NULL)
   14.     └─base withOneRestart(expr, restarts[[1L]])
   15.       └─base doWithOneRestart(return(expr), restart)
  ── Error (test-unsupMI.R:137:3): Plot works ────────────────────────────────────
  <packageNotFoundError/error/condition>
  Error in `loadNamespace(x)`: there is no package called 'ggpubr'
  Backtrace:
      ▆
   1. ├─testthat::expect_s3_class(...) at test-unsupMI.R:137:2
   2. │ └─testthat::quasi_label(enquo(object), arg = "object")
   3. │   └─rlang::eval_bare(expr, quo_get_env(quo))
   4. ├─doMIsaul::plot_MIpca(...)
   5. └─base::loadNamespace(x)
   6.   └─base::withRestarts(stop(cond), retry_loadNamespace = function() NULL)
   7.     └─base withOneRestart(expr, restarts[[1L]])
   8.       └─base doWithOneRestart(return(expr), restart)
  
  [ FAIL 4 | WARN 0 | SKIP 3 | PASS 35 ]
  Error: Test failures
  Execution halted
* checking PDF version of manual ... OK
* checking for non-standard things in the check directory ... OK
* checking for detritus in the temp directory ... OK
* DONE

Status: 2 ERRORs, 1 NOTE
See
  ‘/data/gannet/ripley/R/packages/tests-Suggests/doMIsaul.Rcheck/00check.log’
for details.

Command exited with non-zero status 1
Time 1:52.88, 103.28 + 9.01