diff --git a/cran-comments.Rmd b/cran-comments.Rmd index c0c347a73..a2ff90136 100644 --- a/cran-comments.Rmd +++ b/cran-comments.Rmd @@ -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 @@ -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 @@ -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 -> -> 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 @@ -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 for details. diff --git a/cran-comments.md b/cran-comments.md index ba5700bd7..d5342fbf1 100644 --- a/cran-comments.md +++ b/cran-comments.md @@ -1,16 +1,18 @@ cran-comments ================ -## `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 @@ -24,35 +26,10 @@ build() ``` ``` bash -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 @@ -68,79 +45,19 @@ Status: OK 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 - - 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 - - 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 + 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 - 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 -> -> eval_bare -> exit_handler -> bquote - Execution halted - -This error is in `dplyr` code execution. I don’t think I can solve it. - - mice 3.9.0: PREPERROR - Build ID: mice_3.9.0.tar.gz-9aa8a9462c524b0dad4e60c9f2684fed - Platform: Debian Linux, R-devel, GCC ASAN/UBSAN + Status: succes + + 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 for build mice_3.9.0.tar.gz-9aa8a9462c524b0dad4e60c9f2684fed - Status: success - Duration: 1 hour 34 minutes 26.3 seconds + Status: succes ## Downstream dependencies @@ -159,66 +76,60 @@ revdep_summary() ### README.md -# Platform - -| field | value | -| :------- | :--------------------------- | -| version | R version 4.0.0 (2020-04-24) | -| os | macOS Catalina 10.15.4 | -| 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 | - -# 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 | | | + # Platform + + |field |value | + |:--------|:----------------------------| + |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 |2020-07-13 | + + # Dependencies + + |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