* using log directory ‘/home/hornik/tmp/R.check/r-devel-clang/Work/PKGS/mi.Rcheck’
* using R Under development (unstable) (2025-02-23 r87804)
* using platform: x86_64-pc-linux-gnu
* R was compiled by
    Debian clang version 19.1.7 (1+b1)
    Debian flang-new version 19.1.7 (1+b1)
* running under: Debian GNU/Linux trixie/sid
* using session charset: UTF-8
* checking for file ‘mi/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘mi’ version ‘1.1’
* checking package namespace information ... OK
* checking package dependencies ... OK
* 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 serialization versions ... OK
* checking whether package ‘mi’ can be installed ... OK
See 'https://www.r-project.org/nosvn/R.check/r-devel-linux-x86_64-debian-clang/mi-00install.html' for details.
* checking package directory ... OK
* checking for future file timestamps ... 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 ... [3s/4s] OK
* checking whether the package can be loaded with stated dependencies ... [3s/4s] OK
* checking whether the package can be unloaded cleanly ... [3s/4s] OK
* checking whether the namespace can be loaded with stated dependencies ... [2s/4s] OK
* checking whether the namespace can be unloaded cleanly ... [3s/4s] OK
* checking loading without being on the library search path ... [3s/4s] OK
* checking whether startup messages can be suppressed ... [3s/4s] 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 ... [31s/39s] OK
* checking Rd files ... [1s/1s] NOTE
checkRd: (-1) rdata.frame.Rd:132: Lost braces in \enumerate; \value handles \item{}{} directly
checkRd: (-1) rdata.frame.Rd:133-134: Lost braces in \enumerate; \value handles \item{}{} directly
checkRd: (-1) rdata.frame.Rd:135-137: Lost braces in \enumerate; \value handles \item{}{} directly
checkRd: (-1) rdata.frame.Rd:138-139: Lost braces in \enumerate; \value handles \item{}{} directly
checkRd: (-1) rdata.frame.Rd:144: Lost braces in \enumerate; \value handles \item{}{} directly
checkRd: (-1) rdata.frame.Rd:145-147: Lost braces in \enumerate; \value handles \item{}{} directly
checkRd: (-1) rdata.frame.Rd:148-150: Lost braces in \enumerate; \value handles \item{}{} directly
* checking Rd metadata ... OK
* checking Rd line widths ... OK
* checking Rd cross-references ... NOTE
Found the following Rd file(s) with Rd \link{} targets missing package
anchors:
  02missing_data.frame.Rd: bayesglm
  get_parameters.Rd: polr
  mi2stata.Rd: write.dta
Please provide package anchors for all Rd \link{} targets not in the
package itself and the base packages.
* 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 contents of ‘data’ directory ... OK
* checking data for non-ASCII characters ... [0s/0s] OK
* checking data for ASCII and uncompressed saves ... OK
* checking R/sysdata.rda ... OK
* checking sizes of PDF files under ‘inst/doc’ ... OK
* checking installed files from ‘inst/doc’ ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... [8s/9s] OK
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ... [8s/9s] ERROR
  Running ‘missing_data.frame.R’ [5s/5s]
  Running ‘missing_variable.R’ [3s/3s]
Running the tests in ‘tests/missing_variable.R’ failed.
Complete output:
  > stopifnot(require(mi))
  Loading required package: mi
  Loading required package: Matrix
  Loading required package: stats4
  mi (Version 1.1, packaged: 2022-06-05 05:31:15 UTC; ben)
  mi  Copyright (C) 2008, 2009, 2010, 2011, 2012, 2013, 2014, 2015 Trustees of Columbia University
  This program comes with ABSOLUTELY NO WARRANTY.
  This is free software, and you are welcome to redistribute it
  under the General Public License version 2 or later.
  Execute RShowDoc('COPYING') for details.
  > 
  > x <- rnorm(10)
  > x[1] <- NA
  > y <- missing_variable(x, type = "continuous")
  > 
  > y <- missing_variable(x, type = "irrelevant")
  > x <- rep(1, 10)
  > y <- missing_variable(x, type = "fixed")
  > x <- rep(1:5, each = 2)
  > y <- missing_variable(x, type = "group")
  > 
  > x[1] <- NA
  > y <- missing_variable(x, type = "unordered-categorical")
  > y <- missing_variable(x, type = "ordered-categorical")
  > y <- missing_variable(x, type = "interval")
  > 
  > x <- rbinom(10, size = 1, prob = 0.5)
  > x[1] <- NA
  > y <- missing_variable(x, type = "binary")
  Error in validObject(.Object) : 
    invalid class "binary" object: y : binary variables must have exactly two response categories
  Calls: missing_variable ... .local -> callNextMethod -> .nextMethod -> validObject
  Execution halted
* checking for unstated dependencies in vignettes ... OK
* checking package vignettes ... OK
* checking re-building of vignette outputs ... [0s/1s] OK
* checking PDF version of manual ... [8s/11s] OK
* checking HTML version of manual ... [2s/4s] OK
* checking for non-standard things in the check directory ... OK
* DONE
Status: 1 ERROR, 2 NOTEs