From 11cbbda9db9499069bde7a2c8c3981a5a66a5d9a Mon Sep 17 00:00:00 2001 From: Stef van Buuren Date: Wed, 27 Nov 2024 17:24:59 +0100 Subject: [PATCH] Update cran-comments --- cran-comments.Rmd | 35 ++++++------------------------ cran-comments.md | 54 +++++++++++++++++++++-------------------------- 2 files changed, 31 insertions(+), 58 deletions(-) diff --git a/cran-comments.Rmd b/cran-comments.Rmd index afb98ebc..204820a2 100644 --- a/cran-comments.Rmd +++ b/cran-comments.Rmd @@ -9,6 +9,8 @@ knitr::opts_chunk$set(echo = TRUE) ## Release summary +This is the resubmission of `mice` version 3.17.0. The previous submission was rejected due a problem with the downstream `autoReg` and `finalfit` packages. The problem was a change in the reporting of the confidence intervals. In the previous version confidence intervals were named `2.5 %` and `97.5 %`, a convention inherited from `stats::confint.default`. The update `mice 3.17.0` adopts the more flexible `broom` convention of naming these boundaries `conf.low` and `conf.high`, so that these names work for any probability level. This change caused the two downstream packages to fail. The issue has been fixed in this version of `mice` by duplicating the two conf columns, and naming them `2.5 %` and `97.5 %`. I will alert the maintainers of the `autoReg` and `finalfit` packages to this change, but for now, having the duplicate columns fixes the problem. + This release of `mice` adds new features, bug fixes, and documentation improvements. See @@ -73,45 +75,22 @@ revdep_check(pkg = ".", num_workers = 12, quiet = FALSE) revdepcheck::revdep_summary() ``` -### Summary +### revdepcheck results We checked 123 reverse dependencies (118 from CRAN + 5 from Bioconductor), comparing R CMD check results across CRAN and dev versions of this package. - * We saw 3 new problems + * We saw 1 new problems * We failed to check 3 packages Issues with CRAN packages are summarised below. -### New problems (3) - -|package |version |error |warning |note | -|:--------|:-------|:------|:-------|:---------| -|[autoReg](problems.md#autoreg)|0.3.3 |__+2__ | | | -|[bipd](problems.md#bipd)|0.3 |1 | |-1 __+1__ | -|[finalfit](problems.md#finalfit)|1.0.8 |__+2__ | |1 | - +### New problems (This reports the first line of each new failure) -* autoReg - checking examples ... ERROR - checking running R code from vignettes ... - * bipd - checking dependencies in R code ...sh: line 1: 24340 Segmentation fault: 11 R_DEFAULT_PACKAGES=NULL '/Library/Frameworks/R.framework/Resources/bin/R' --vanilla --no-echo 2>&1 < '/var/folders/5_/g85d42yj50b6lrjq4rzjzg8w0000gn/T//RtmpazqvFP/file5c206c170a3d' - -* finalfit - checking examples ... ERROR - checking running R code from vignettes ... - -mice developer comment: These new problems are unrelated to mice - -### Failed to check (3) + checking dependencies in R code ...sh: line 1: 58727 Segmentation fault: 11 R_DEFAULT_PACKAGES=NULL '/Library/Frameworks/R.framework/Resources/bin/R' --vanilla --no-echo 2>&1 < '/var/folders/5_/g85d42yj50b6lrjq4rzjzg8w0000gn/T//RtmpM38C1S/filee1cf761be8f7' -|package |version |error |warning |note | -|:-------|:----------|:-----|:-------|:----| -|brms |2.22.0 |1 | |2 | -|dynr |0.1.16-105 |1 | | | -|rmsb |1.1-1 |1 | |1 | +### Failed to check * brms (NA) * dynr (NA) diff --git a/cran-comments.md b/cran-comments.md index 107071ac..311b2015 100644 --- a/cran-comments.md +++ b/cran-comments.md @@ -3,6 +3,20 @@ cran-comments ## Release summary +This is the resubmission of `mice` version 3.17.0. The previous +submission was rejected due a problem with the downstream `autoReg` and +`finalfit` packages. The problem was a change in the reporting of the +confidence intervals. In the previous version confidence intervals were +named `2.5 %` and `97.5 %`, a convention inherited from +`stats::confint.default`. The update `mice 3.17.0` adopts the more +flexible `broom` convention of naming these boundaries `conf.low` and +`conf.high`, so that these names work for any probability level. This +change caused the two downstream packages to fail. The issue has been +fixed in this version of `mice` by duplicating the two conf columns, and +naming them `2.5 %` and `97.5 %`. I will alert the maintainers of the +`autoReg` and `finalfit` packages to this change, but for now, having +the duplicate columns fixes the problem. + This release of `mice` adds new features, bug fixes, and documentation improvements. See @@ -76,7 +90,7 @@ revdepcheck::revdep_summary() ## ✔ accelmissing 1.4 ── E: 0 | W: 0 | N: 1 ## ✔ adjustedCurves 0.11.2 ── E: 0 | W: 0 | N: 0 ## ✔ alookr 0.3.9 ── E: 0 | W: 0 | N: 0 - ## ✖ autoReg 0.3.3 ── E: 0 +2 | W: 0 | N: 0 + ## ✔ autoReg 0.3.3 ── E: 0 | W: 0 | N: 0 ## ✔ BaM 1.0.3 ── E: 0 | W: 0 | N: 0 ## ✔ basecamb 1.1.5 ── E: 0 | W: 0 | N: 0 ## ✔ betaMC 1.3.2 ── E: 0 | W: 0 | N: 0 @@ -97,12 +111,12 @@ revdepcheck::revdep_summary() ## ✔ dynamite 1.5.5 ── E: 0 | W: 0 | N: 2 ## I dynr 0.1.16.105 ── E: 1 | W: 0 | N: 0 ## ✔ eatRep 0.14.7 ── E: 0 | W: 0 | N: 0 - ## ✖ finalfit 1.0.8 ── E: 0 +2 | W: 0 | N: 1 + ## ✔ finalfit 1.0.8 ── E: 0 | W: 0 | N: 1 ## ✔ FLAME 2.1.1 ── E: 0 | W: 0 | N: 0 ## ✔ flevr 0.0.4 ── E: 0 | W: 0 | N: 0 ## ✔ gerbil 0.1.9 ── E: 0 | W: 0 | N: 0 ## ✔ gFormulaMI 1.0.0 ── E: 0 | W: 0 | N: 0 - ## ✔ ggeffects 1.7.2 ── E: 0 | W: 0 | N: 0 + ## ✔ ggeffects 2.0.0 ── E: 0 | W: 0 | N: 0 ## ✔ ggmice 0.1.0 ── E: 0 | W: 0 | N: 0 ## ✔ gtsummary 2.0.3 ── E: 0 | W: 0 | N: 0 ## ✔ HardyWeinberg 1.7.8 ── E: 0 | W: 0 | N: 0 @@ -162,7 +176,7 @@ revdepcheck::revdep_summary() ## ✔ nncc 2.0.0 ── E: 0 | W: 0 | N: 0 ## ✔ ordbetareg 0.7.2 ── E: 0 | W: 0 | N: 2 ## ✔ OTrecod 0.1.2 ── E: 0 | W: 0 | N: 1 - ## ✔ parameters 0.23.0 ── E: 1 | W: 0 | N: 0 + ## ✔ parameters 0.24.0 ── E: 0 | W: 0 | N: 0 ## ✔ pema 0.1.3 ── E: 1 | W: 0 | N: 2 ## ✔ pre 1.0.7 ── E: 0 | W: 0 | N: 0 ## ✔ psfmi 1.4.0 ── E: 0 | W: 0 | N: 0 @@ -197,48 +211,28 @@ revdepcheck::revdep_summary() ## ✔ vsmi 0.1.0 ── E: 0 | W: 0 | N: 0 ## ✔ weights 1.0.4 ── E: 0 | W: 0 | N: 0 -### Summary +### revdepcheck results We checked 123 reverse dependencies (118 from CRAN + 5 from Bioconductor), comparing R CMD check results across CRAN and dev versions of this package. -- We saw 3 new problems +- We saw 1 new problems - We failed to check 3 packages Issues with CRAN packages are summarised below. -### New problems (3) - -| package | version | error | warning | note | -|:---------------------------------|:--------|:-------|:--------|:----------| -| [autoReg](problems.md#autoreg) | 0.3.3 | **+2** | | | -| [bipd](problems.md#bipd) | 0.3 | 1 | | -1 **+1** | -| [finalfit](problems.md#finalfit) | 1.0.8 | **+2** | | 1 | +### New problems (This reports the first line of each new failure) -- autoReg checking examples … ERROR checking running R code from - vignettes … - -- bipd checking dependencies in R code …sh: line 1: 24340 Segmentation +- bipd checking dependencies in R code …sh: line 1: 58727 Segmentation fault: 11 R_DEFAULT_PACKAGES=NULL ‘/Library/Frameworks/R.framework/Resources/bin/R’ –vanilla –no-echo 2\>&1 \< - ‘/var/folders/5\_/g85d42yj50b6lrjq4rzjzg8w0000gn/T//RtmpazqvFP/file5c206c170a3d’ - -- finalfit checking examples … ERROR checking running R code from - vignettes … - -mice developer comment: These new problems are unrelated to mice - -### Failed to check (3) + ‘/var/folders/5\_/g85d42yj50b6lrjq4rzjzg8w0000gn/T//RtmpM38C1S/filee1cf761be8f7’ -| package | version | error | warning | note | -|:--------|:-----------|:------|:--------|:-----| -| brms | 2.22.0 | 1 | | 2 | -| dynr | 0.1.16-105 | 1 | | | -| rmsb | 1.1-1 | 1 | | 1 | +### Failed to check - brms (NA) - dynr (NA)