From 64a1639205c1e7d9e17055fcf1211d9383fee7dd Mon Sep 17 00:00:00 2001 From: Stef van Buuren Date: Wed, 27 Jan 2021 10:48:04 +0100 Subject: [PATCH] Prepare 3.13.0 for CRAN --- cran-comments.Rmd | 107 +++++++++----------------------- cran-comments.md | 152 +++++++++++++--------------------------------- 2 files changed, 70 insertions(+), 189 deletions(-) diff --git a/cran-comments.Rmd b/cran-comments.Rmd index b32e6c77e..cf4b81998 100644 --- a/cran-comments.Rmd +++ b/cran-comments.Rmd @@ -7,17 +7,17 @@ output: github_document knitr::opts_chunk$set(echo = TRUE) ``` -## mice 3.12.0 +## mice 3.13.0 New submission. ## Reason -`mice 3.12.0` implements important new features and contains bug fixes. +After signal sent by Brian Ripley on Jan26. `mice 3.13.0` implements a fix for a bug that produced errors with `mitml 0.4-0`. ## Test environments -* local OS X install, 10.15.7, R 4.0.3 +* local OS X install, 11.11, R 4.0.3 * win-builder * Rhub @@ -31,7 +31,7 @@ build() ``` ```{bash eval=FALSE} -R CMD CHECK mice_3.12.0.tar.gz +R CMD CHECK mice_3.13.0.tar.gz ``` @@ -54,10 +54,10 @@ check_rhub() Results: -1. Debian Linux, R-devel, GCC ASAN/UBSAN: : Error, possibly related to an installing problem of miceadds package -2. Windows Server 2008 R2 SP1, R-devel, 32/64 bit: : Success -3. Ubuntu Linux 16.04 LTS, R-release, GCC: : Success -4. Fedora Linux, R-devel, clang, gfortran: : Error, likely to be unrelated to mice +1. Debian Linux, R-devel, GCC ASAN/UBSAN: Error, compilation failed for package `miceadds` +2. Windows Server 2008 R2 SP1, R-devel, 32/64 bit: Finished: SUCCESS +3. Ubuntu Linux 20.04.1 LTS, R-release, GCC: Success +4. Fedora Linux, R-devel, clang, gfortran: Success, with four (benign) warnings about CPU time for examples ## Downstream dependencies @@ -72,47 +72,12 @@ revdep_check(num_workers = 10) ### `failures.md` -There are one new failure (`brms`) and one old (`dynr`). Both failures are caused by -installation problems on the test servers. These failure do not seem to be related to `mice`. +There is one old failure (`dynr`): `configure: error: gsl-config not found, is GSL installed?` +Not related to `mice`. ### `problems.md` -There are new warnings in several packages because `mice 3.12.0` exports a new -`filter.mids()` method for the `dplyr::filter()` generic. For example, we -get `Warning: replacing previous import ‘mice::filter’ by ‘stats::filter’ when loading ‘BaM’`. -Sometimes we get the reverse message. I noted the package authors the upcoming -change in mice on Oct 29. Affected packages: -`BaM`, `genpathmox`, `idem`, `misaem`, `Qtools`, `TestDataImputation` - -Here's the mail: - ---- - -R packages: BaM, genpathmox, idem, misaem, Qtools, TestDataImputation - -Dear package maintainer, - -A reversed dependency check revealed a new warning in your package that results from the upcoming release mice 3.12.0. The new release exports a new `filter.mids()` method for the `dplyr::filter()` generic. - -I get: `Warning: replacing previous import ‘mice::filter’ by ‘stats::filter’ when loading ‘BaM’` and others. For Qtools I get the reverse: Warning: replacing previous import ‘stats::filter’ by ‘mice::filter’ when loading ‘Qtools’. - -The warning is probably benign, but please check in your package if the introduction of `mice::filter.mids()` would inadvertent change a call to `stats::filter()` to `dplyr::filter()` or vice versa. If this happens, please update your import directive. - -I intend to submit to CRAN in about one week. Hope this helps to evade surprises when mice 3.12.0 hits CRAN. - -Best wishes, Stef - ---- - -Update Nov 9: The package maintainers of `BaM` and `Qtools` told me that the planned mice update did not affect the validity of their packages. Did not see a reaction from other maintainers. - -A second problem concerned to `miceadds` package. This package uses -`mice::.pmm.match`, which I had removed because I thought nobody used it -anymore. I will put it back in. - -Update Nov 9: `mice::.pmm.match` is now again part of the `mice` package - -The `idem` package yields two notes. Neither of these is related to `mice`. +*Wow, no problems at all. :)* ### README.md @@ -121,69 +86,55 @@ The `idem` package yields two notes. Neither of these is related to `mice`. |field |value | |:--------|:----------------------------| -|version |R version 4.0.2 (2020-06-22) | -|os |macOS Catalina 10.15.7 | +|version |R version 4.0.3 (2020-10-10) | +|os |macOS Big Sur 10.16 | |system |x86_64, darwin17.0 | |ui |RStudio | |language |(EN) | |collate |en_US.UTF-8 | |ctype |en_US.UTF-8 | |tz |Europe/Amsterdam | -|date |2020-10-29 | +|date |2021-01-26 | # Dependencies |package |old |new |Δ | |:----------|:------|:------|:--| -|mice |3.11.0 |3.12.0 |* | +|mice |3.12.0 |3.13.0 |* | |assertthat |0.2.1 |0.2.1 | | -|backports |1.1.10 |1.1.10 | | -|broom |0.7.2 |0.7.2 | | -|cli |2.1.0 |2.1.0 | | -|cpp11 |0.2.3 |0.2.3 | | +|backports |1.2.1 |1.2.1 | | +|broom |0.7.3 |0.7.3 | | +|cli |2.2.0 |2.2.0 | | +|cpp11 |0.2.5 |0.2.5 | | |crayon |1.3.4 |1.3.4 | | |digest |0.6.27 |0.6.27 | | -|dplyr |1.0.2 |1.0.2 | | +|dplyr |1.0.3 |1.0.3 | | |ellipsis |0.3.1 |0.3.1 | | -|fansi |0.4.1 |0.4.1 | | -|generics |0.0.2 |0.0.2 | | +|fansi |0.4.2 |0.4.2 | | +|generics |0.1.0 |0.1.0 | | |glue |1.4.2 |1.4.2 | | |lifecycle |0.2.0 |0.2.0 | | -|magrittr |1.5 |1.5 | | -|pillar |1.4.6 |1.4.6 | | +|magrittr |2.0.1 |2.0.1 | | +|pillar |1.4.7 |1.4.7 | | |pkgconfig |2.0.3 |2.0.3 | | |purrr |0.3.4 |0.3.4 | | |R6 |2.5.0 |2.5.0 | | -|Rcpp |1.0.5 |1.0.5 | | -|rlang |0.4.8 |0.4.8 | | +|Rcpp |1.0.6 |1.0.6 | | +|rlang |0.4.10 |0.4.10 | | |stringi |1.5.3 |1.5.3 | | |stringr |1.4.0 |1.4.0 | | -|tibble |3.0.4 |3.0.4 | | +|tibble |3.0.5 |3.0.5 | | |tidyr |1.1.2 |1.1.2 | | |tidyselect |1.1.0 |1.1.0 | | |utf8 |1.1.4 |1.1.4 | | -|vctrs |0.3.4 |0.3.4 | | +|vctrs |0.3.6 |0.3.6 | | # Revdeps -## Failed to check (2) +## Failed to check (1) |package |version |error |warning |note | |:-------|:---------|:-----|:-------|:----| -|brms |? | | | | |dynr |0.1.15-25 |1 | | | - -## New problems (7) - -|package |version |error |warning |note | -|:----------------------------------------------------|:-------|:-----|:-------|:--------| -|[BaM](problems.md#bam) |1.0.1 | |__+1__ | | -|[genpathmox](problems.md#genpathmox) |0.4 | |__+1__ | | -|[idem](problems.md#idem) |5.0 | |__+1__ |2 | -|[miceadds](problems.md#miceadds) |3.10-28 | | |2 __+1__ | -|[misaem](problems.md#misaem) |1.0.0 | |__+1__ | | -|[Qtools](problems.md#qtools) |1.5.2 | |__+1__ | | -|[TestDataImputation](problems.md#testdataimputation) |1.1 | |__+1__ | | ``` -This package requires additional software to be installed. See for details. diff --git a/cran-comments.md b/cran-comments.md index 9d0cb68b1..1ecb6b9a4 100644 --- a/cran-comments.md +++ b/cran-comments.md @@ -1,19 +1,20 @@ cran-comments ================ -## mice 3.12.0 +## mice 3.13.0 New submission. ## Reason -`mice 3.12.0` implements important new features and contains bug fixes. +After signal sent by Brian Ripley on Jan26. `mice 3.13.0` implements a +fix for a bug that produced errors with `mitml 0.4-0`. ## Test environments - - local OS X install, 10.15.7, R 4.0.3 - - win-builder - - Rhub +- local OS X install, 11.11, R 4.0.3 +- win-builder +- Rhub ## Local check @@ -25,7 +26,7 @@ build() ``` ``` bash -R CMD CHECK mice_3.12.0.tar.gz +R CMD CHECK mice_3.13.0.tar.gz ``` Status: OK @@ -46,18 +47,12 @@ check_rhub() Results: -1. Debian Linux, R-devel, GCC ASAN/UBSAN: - : - Error, possibly related to an installing problem of miceadds package -2. Windows Server 2008 R2 SP1, R-devel, 32/64 bit: - : - Success -3. Ubuntu Linux 16.04 LTS, R-release, GCC: - : - Success -4. Fedora Linux, R-devel, clang, gfortran: - : - Error, likely to be unrelated to mice +1. Debian Linux, R-devel, GCC ASAN/UBSAN: Error, compilation failed for + package `miceadds` +2. Windows Server 2008 R2 SP1, R-devel, 32/64 bit: Finished: SUCCESS +3. Ubuntu Linux 20.04.1 LTS, R-release, GCC: Success +4. Fedora Linux, R-devel, clang, gfortran: Success, with four (benign) + warnings about CPU time for examples ## Downstream dependencies @@ -71,132 +66,67 @@ revdep_check(num_workers = 10) ### `failures.md` -There are one new failure (`brms`) and one old (`dynr`). Both failures -are caused by installation problems on the test servers. These failure -do not seem to be related to `mice`. +There is one old failure (`dynr`): +`configure: error: gsl-config not found, is GSL installed?` Not related +to `mice`. ### `problems.md` -There are new warnings in several packages because `mice 3.12.0` exports -a new `filter.mids()` method for the `dplyr::filter()` generic. For -example, we get `Warning: replacing previous import ‘mice::filter’ by -‘stats::filter’ when loading ‘BaM’`. Sometimes we get the reverse -message. I noted the package authors the upcoming change in mice on Oct -29. Affected packages: `BaM`, `genpathmox`, `idem`, `misaem`, `Qtools`, -`TestDataImputation` - -Here’s the mail: - ------ - -R packages: BaM, genpathmox, idem, misaem, Qtools, TestDataImputation - -Dear package maintainer, - -A reversed dependency check revealed a new warning in your package that -results from the upcoming release mice 3.12.0. The new release exports a -new `filter.mids()` method for the `dplyr::filter()` generic. - -I get: `Warning: replacing previous import ‘mice::filter’ by -‘stats::filter’ when loading ‘BaM’` and others. For Qtools I get the -reverse: Warning: replacing previous import ‘stats::filter’ by -‘mice::filter’ when loading ‘Qtools’. - -The warning is probably benign, but please check in your package if the -introduction of `mice::filter.mids()` would inadvertent change a call to -`stats::filter()` to `dplyr::filter()` or vice versa. If this happens, -please update your import directive. - -I intend to submit to CRAN in about one week. Hope this helps to evade -surprises when mice 3.12.0 hits CRAN. - -Best wishes, Stef - ------ - -Update Nov 9: The package maintainers of `BaM` and `Qtools` told me that -the planned mice update did not affect the validity of their packages. -Did not see a reaction from other maintainers. - -A second problem concerned to `miceadds` package. This package uses -`mice::.pmm.match`, which I had removed because I thought nobody used it -anymore. I will put it back in. - -Update Nov 9: `mice::.pmm.match` is now again part of the `mice` package - -The `idem` package yields two notes. Neither of these is related to -`mice`. +*Wow, no problems at all. :)* ### README.md # Platform - + |field |value | |:--------|:----------------------------| - |version |R version 4.0.2 (2020-06-22) | - |os |macOS Catalina 10.15.7 | + |version |R version 4.0.3 (2020-10-10) | + |os |macOS Big Sur 10.16 | |system |x86_64, darwin17.0 | |ui |RStudio | |language |(EN) | |collate |en_US.UTF-8 | |ctype |en_US.UTF-8 | |tz |Europe/Amsterdam | - |date |2020-10-29 | - + |date |2021-01-26 | + # Dependencies - + |package |old |new |Δ | |:----------|:------|:------|:--| - |mice |3.11.0 |3.12.0 |* | + |mice |3.12.0 |3.13.0 |* | |assertthat |0.2.1 |0.2.1 | | - |backports |1.1.10 |1.1.10 | | - |broom |0.7.2 |0.7.2 | | - |cli |2.1.0 |2.1.0 | | - |cpp11 |0.2.3 |0.2.3 | | + |backports |1.2.1 |1.2.1 | | + |broom |0.7.3 |0.7.3 | | + |cli |2.2.0 |2.2.0 | | + |cpp11 |0.2.5 |0.2.5 | | |crayon |1.3.4 |1.3.4 | | |digest |0.6.27 |0.6.27 | | - |dplyr |1.0.2 |1.0.2 | | + |dplyr |1.0.3 |1.0.3 | | |ellipsis |0.3.1 |0.3.1 | | - |fansi |0.4.1 |0.4.1 | | - |generics |0.0.2 |0.0.2 | | + |fansi |0.4.2 |0.4.2 | | + |generics |0.1.0 |0.1.0 | | |glue |1.4.2 |1.4.2 | | |lifecycle |0.2.0 |0.2.0 | | - |magrittr |1.5 |1.5 | | - |pillar |1.4.6 |1.4.6 | | + |magrittr |2.0.1 |2.0.1 | | + |pillar |1.4.7 |1.4.7 | | |pkgconfig |2.0.3 |2.0.3 | | |purrr |0.3.4 |0.3.4 | | |R6 |2.5.0 |2.5.0 | | - |Rcpp |1.0.5 |1.0.5 | | - |rlang |0.4.8 |0.4.8 | | + |Rcpp |1.0.6 |1.0.6 | | + |rlang |0.4.10 |0.4.10 | | |stringi |1.5.3 |1.5.3 | | |stringr |1.4.0 |1.4.0 | | - |tibble |3.0.4 |3.0.4 | | + |tibble |3.0.5 |3.0.5 | | |tidyr |1.1.2 |1.1.2 | | |tidyselect |1.1.0 |1.1.0 | | |utf8 |1.1.4 |1.1.4 | | - |vctrs |0.3.4 |0.3.4 | | - + |vctrs |0.3.6 |0.3.6 | | + # Revdeps - - ## Failed to check (2) - + + ## Failed to check (1) + |package |version |error |warning |note | |:-------|:---------|:-----|:-------|:----| - |brms |? | | | | |dynr |0.1.15-25 |1 | | | - - ## New problems (7) - - |package |version |error |warning |note | - |:----------------------------------------------------|:-------|:-----|:-------|:--------| - |[BaM](problems.md#bam) |1.0.1 | |__+1__ | | - |[genpathmox](problems.md#genpathmox) |0.4 | |__+1__ | | - |[idem](problems.md#idem) |5.0 | |__+1__ |2 | - |[miceadds](problems.md#miceadds) |3.10-28 | | |2 __+1__ | - |[misaem](problems.md#misaem) |1.0.0 | |__+1__ | | - |[Qtools](problems.md#qtools) |1.5.2 | |__+1__ | | - |[TestDataImputation](problems.md#testdataimputation) |1.1 | |__+1__ | | - -This package requires additional software to be installed. See - for -details.