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@stefvanbuuren
stefvanbuuren committed Jul 13, 2020
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Expand Up @@ -7,15 +7,16 @@ output: github_document
knitr::opts_chunk$set(echo = TRUE)
```

## `mice 3.9.0`, new submission
## mice 3.10
New submission

## Reason

This update `mice 3.9.0` adds new functionality, reduces dependencies and provides solutions for issues found in `mice 3.8.0` and before.
`mice 3.10.0` adds new functions `tidy.mipo()` and `glance.mipo()`, and solves a problem caused by separating `broom` and `broom.mixed`.

## Test environments

* local OS X install, 10.15.4, R 4.0.0
* local OS X install, 10.15.4, R 4.0.2
* win-builder
* Rhub

Expand All @@ -29,36 +30,11 @@ build()
```

```{bash eval=FALSE}
R CMD CHECK /Users/buurensv/Package/mice/mice_3.9.0.tar.gz
R CMD CHECK /Users/buurensv/Package/mice/mice_3.10.0.tar.gz
```

Fails, although interactive building in Rstudio works fine

```
* installing *source* package ‘mice’ ...
** using staged installation
** libs
clang++ -mmacosx-version-min=10.13 -std=gnu++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I'/Users/buurensv/Library/R/3.6/library/Rcpp/include' -I/usr/local/include -fPIC -Wall -g -O2 -c RcppExports.cpp -o RcppExports.o
clang++ -mmacosx-version-min=10.13 -std=gnu++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I'/Users/buurensv/Library/R/3.6/library/Rcpp/include' -I/usr/local/include -fPIC -Wall -g -O2 -c match.cpp -o match.o
Error: package ‘Rcpp’ was installed before R 4.0.0: please re-install it
Execution halted
clang++ -mmacosx-version-min=10.13 -std=gnu++11 -dynamiclib -Wl,-headerpad_max_install_names -undefined dynamic_lookup -single_module -multiply_defined suppress -L/Library/Frameworks/R.framework/Resources/lib -L/usr/local/lib -o mice.so RcppExports.o match.o -F/Library/Frameworks/R.framework/.. -framework R -Wl,-framework -Wl,CoreFoundation
Error: package ‘Rcpp’ was installed before R 4.0.0: please re-install it
Execution halted
installing to /Users/buurensv/Dropbox/Package/mice/mice/mice.Rcheck/00LOCK-mice/00new/mice/libs
** R
** data
*** moving datasets to lazyload DB
** inst
** byte-compile and prepare package for lazy loading
Error: package ‘broom’ was installed before R 4.0.0: please re-install it
Execution halted
ERROR: lazy loading failed for package ‘mice’
* removing ‘/Users/buurensv/Dropbox/Package/mice/mice/mice.Rcheck/mice’
```

I do not understand this message. After upgrading the `R 4.0.0`, I refreshed all packages, as required. Re-installing `Rcpp` manually did not solve the problem. I will assume it is a false positive.

Status: OK

## win-builder

Expand All @@ -76,86 +52,23 @@ check_rhub()
```

```
mice 3.9.0: NOTE
Build ID: mice_3.9.0.tar.gz-96a5a0f7e247483493124db3ee412d47
Platform: Windows Server 2008 R2 SP1, R-devel, 32/64 bit
* checking examples ...
** running examples for arch 'i386' ... NOTE
Examples with CPU (user + system) or elapsed time > 5s
D1 5.58 0.05 5.68
user system elapsed
** running examples for arch 'x64' ... NOTE
Examples with CPU (user + system) or elapsed time > 5s
user system elapsed
D1 5.7 0.06 5.77
```
Build ID: mice_3.10.0.tar.gz-ad5f8a9c8d27d823a9c47247b8a27a39
Platform: Debian Linux, R-devel, GCC
Submitted: 58 minutes 23 seconds ago
Build time: 57 minutes 56.7 seconds
```
mice 3.9.0: NOTE
Build ID: mice_3.9.0.tar.gz-76d8ae5abbb941fc816b6716061457f4
Platform: Ubuntu Linux 16.04 LTS, R-release, GCC
* checking examples ... NOTE
Examples with CPU or elapsed time > 5s
user system elapsed
D1 3.908 0.136 7.817
D3 3.036 0.044 6.117
D2 3.000 0.020 5.797
** found \donttest examples: check also with --run-donttest
Status: succes
```

```
mice 3.9.0: ERROR
Build ID: mice_3.9.0.tar.gz-91b0be74f9784bf484650eebf312a8b8
Platform: Fedora Linux, R-devel, clang, gfortran
* checking examples ... ERROR
Running examples in ‘mice-Ex.R’ failed
The error most likely occurred in:
> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: mice.impute.2l.bin
> ### Title: Imputation by a two-level logistic model using 'glmer'
> ### Aliases: mice.impute.2l.bin
> ### Keywords: datagen
>
> ### ** Examples
>
> library(tidyr)
> library(dplyr)
Attaching package: ‘dplyr’
The following objects are masked from ‘package:stats’:
filter, lag
The following objects are masked from ‘package:base’:
intersect, setdiff, setequal, union
> data("toenail2")
> data <- tidyr::complete(toenail2, patientID, visit) %>%
+ tidyr::fill(treatment) %>%
+ dplyr::select(-time) %>%
+ dplyr::mutate(patientID = as.integer(patientID))
Error in bquote(on.exit({ : 'where' must be an environment
Calls: %>% ... replace_na -> <Anonymous> -> eval_bare -> exit_handler -> bquote
Execution halted
```

This error is in `dplyr` code execution. I don't think I can solve it.
Build ID: mice_3.10.0.tar.gz-c5935e091347f67ee83d2577042c897d
Platform: Debian Linux, R-devel, GCC
Submitted: 28 minutes 51.1 seconds ago
Build time: 28 minutes 49 seconds
Status: succes
```
mice 3.9.0: PREPERROR
Build ID: mice_3.9.0.tar.gz-9aa8a9462c524b0dad4e60c9f2684fed
Platform: Debian Linux, R-devel, GCC ASAN/UBSAN

Status for build mice_3.9.0.tar.gz-9aa8a9462c524b0dad4e60c9f2684fed
Status: success
Duration: 1 hour 34 minutes 26.3 seconds
```

## Downstream dependencies

Expand All @@ -176,65 +89,61 @@ revdep_summary()

### README.md

```
# Platform
|field |value |
|:--------|:----------------------------|
|version |R version 4.0.0 (2020-04-24) |
|os |macOS Catalina 10.15.4 |
|version |R version 4.0.2 (2020-06-22) |
|os |macOS Catalina 10.15.5 |
|system |x86_64, darwin17.0 |
|ui |RStudio |
|language |(EN) |
|collate |en_US.UTF-8 |
|ctype |en_US.UTF-8 |
|tz |Europe/Amsterdam |
|date |2020-05-14 |
|date |2020-07-13 |
# Dependencies
|package |old |new |Δ |
|:----------|:--------|:--------|:--|
|mice |3.8.0 |3.9.0 |* |
|assertthat |0.2.1 |0.2.1 | |
|backports |1.1.7 |1.1.7 | |
|BH |1.72.0-3 |1.72.0-3 | |
|broom |0.5.6 |0.5.6 | |
|cli |2.0.2 |2.0.2 | |
|crayon |1.3.4 |1.3.4 | |
|digest |0.6.25 |0.6.25 | |
|dplyr |0.8.5 |0.8.5 | |
|ellipsis |0.3.0 |0.3.0 | |
|fansi |0.4.1 |0.4.1 | |
|generics |0.0.2 |0.0.2 | |
|glue |1.4.1 |1.4.1 | |
|lifecycle |0.2.0 |0.2.0 | |
|magrittr |1.5 |1.5 | |
|pillar |1.4.4 |1.4.4 | |
|pkgconfig |2.0.3 |2.0.3 | |
|plogr |0.2.0 |0.2.0 | |
|plyr |1.8.6 |1.8.6 | |
|purrr |0.3.4 |0.3.4 | |
|R6 |2.4.1 |2.4.1 | |
|Rcpp |1.0.4.6 |1.0.4.6 | |
|reshape2 |1.4.4 |1.4.4 | |
|rlang |0.4.6 |0.4.6 | |
|stringi |1.4.6 |1.4.6 | |
|stringr |1.4.0 |1.4.0 | |
|tibble |3.0.1 |3.0.1 | |
|tidyr |1.0.3 |1.0.3 | |
|tidyselect |1.1.0 |1.1.0 | |
|utf8 |1.1.4 |1.1.4 | |
|vctrs |0.3.0 |0.3.0 | |

## Revdeps

### Failed to check (4)

|package |version |error |warning |note |
|:--------------|:---------|:-----|:-------|:----|
|brms |2.12.0 |1 | |1 |
|dynr |0.1.15-25 |1 | | |
|MissingDataGUI |0.2-5 |1 | | |
|Replication |0.1.2 |1 | | |
|package |old |new |Δ |
|:----------|:------|:------|:--|
|mice |3.9.0 |3.10.0 |* |
|assertthat |0.2.1 |0.2.1 | |
|backports |1.1.8 |1.1.8 | |
|broom |0.7.0 |0.7.0 | |
|cli |2.0.2 |2.0.2 | |
|crayon |1.3.4 |1.3.4 | |
|digest |0.6.25 |0.6.25 | |
|dplyr |1.0.0 |1.0.0 | |
|ellipsis |0.3.1 |0.3.1 | |
|fansi |0.4.1 |0.4.1 | |
|generics |0.0.2 |0.0.2 | |
|glue |1.4.1 |1.4.1 | |
|lifecycle |0.2.0 |0.2.0 | |
|magrittr |1.5 |1.5 | |
|pillar |1.4.6 |1.4.6 | |
|pkgconfig |2.0.3 |2.0.3 | |
|purrr |0.3.4 |0.3.4 | |
|R6 |2.4.1 |2.4.1 | |
|Rcpp |1.0.5 |1.0.5 | |
|rlang |0.4.7 |0.4.7 | |
|stringi |1.4.6 |1.4.6 | |
|stringr |1.4.0 |1.4.0 | |
|tibble |3.0.3 |3.0.3 | |
|tidyr |1.1.0 |1.1.0 | |
|tidyselect |1.1.0 |1.1.0 | |
|utf8 |1.1.4 |1.1.4 | |
|vctrs |0.3.1 |0.3.1 | |
# Revdeps
## Failed to check (2)
|package |version |error |warning |note |
|:-----------|:---------|:-----|:-------|:----|
|dynr |0.1.15-25 |1 | | |
|Replication |0.1.2 |1 | | |
```

These package require additional software to be installed. See <https://github.com/stefvanbuuren/mice/blob/master/revdep/failures.md> for details.
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