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 https://github.com/amices/mice/blob/master/NEWS.md
packageVersion("mice")## [1] '3.17.0'
R.Version()$version.string## [1] "R version 4.4.2 (2024-10-31)"
NOTE: Run in OSX terminal, not in Rstudio terminal.
env _R_CHECK_DEPENDS_ONLY_=true R CMD check mice_3.17.0.tar.gz
Status: OKdevtools::check(env_vars = c('_R_CHECK_DEPENDS_ONLY_' = "true"))
...
Status: OKdevtools::check_win_devel()
Status: OKrhub::rhub_doctor()
rhub::rhub_check()Status: OK <>
For details: https://github.com/amices/mice/actions
Note: Inactivate credentials::set_github_pat()
library(revdepcheck)
revdep_reset()
revdep_check(pkg = ".", num_workers = 12, quiet = FALSE)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 | 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
## ✔ BGGM 2.1.3 ── E: 0 | W: 0 | N: 1
## ✖ bipd 0.3 ── E: 1 | W: 0 | N: 0-1+1
## ✔ bootImpute 1.2.1 ── E: 1 | W: 0 | N: 0
## T brms 2.22.0 ── E: 1 | W: 0 | N: 2
## ✔ brokenstick 2.5.0 ── E: 0 | W: 0 | N: 0
## ✔ broom.helpers 1.17.0 ── E: 0 | W: 0 | N: 0
## ✔ cati 0.99.4 ── E: 0 | W: 0 | N: 0
## ✔ censcyt 1.14.0 ── E: 0 | W: 0 | N: 3
## ✔ CIMPLE 0.1.0 ── E: 0 | W: 0 | N: 0
## ✔ ClustAll 1.2.0 ── E: 0 | W: 0 | N: 0
## ✔ clusterMI 1.2.2 ── E: 0 | W: 0 | N: 0
## ✔ cmahalanobis 0.4.2 ── E: 0 | W: 0 | N: 0
## ✔ cobalt 4.5.5 ── E: 0 | W: 0 | N: 0
## ✔ dlookr 0.6.3 ── E: 0 | W: 0 | N: 0
## ✔ 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 | 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 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
## ✔ hhsmm 0.4.2 ── E: 0 | W: 0 | N: 0
## ✔ Hmisc 5.2.0 ── E: 0 | W: 0 | N: 1
## ✔ holodeck 0.2.2 ── E: 0 | W: 0 | N: 0
## ✔ hot.deck 1.2 ── E: 0 | W: 0 | N: 1
## ✔ howManyImputations 0.2.5 ── E: 0 | W: 0 | N: 0
## ✔ HSAUR3 1.0.15 ── E: 0 | W: 0 | N: 0
## ✔ idem 5.2 ── E: 0 | W: 0 | N: 2
## ✔ ImputeRobust 1.3.1 ── E: 0 | W: 0 | N: 0
## ✔ insight 1.0.0 ── E: 0 | W: 0 | N: 0
## ✔ intmed 0.1.2 ── E: 0 | W: 0 | N: 0
## ✔ IPWboxplot 0.1.2 ── E: 0 | W: 0 | N: 0
## ✔ joinet 1.0.0 ── E: 1 | W: 0 | N: 1
## ✔ JWileymisc 1.4.1 ── E: 0 | W: 0 | N: 0
## ✔ konfound 1.0.2 ── E: 0 | W: 0 | N: 0
## ✔ LMMstar 1.1.0 ── E: 0 | W: 0 | N: 1
## ✔ logistf 1.26.0 ── E: 0 | W: 0 | N: 0
## ✔ LSAmitR 1.0.3 ── E: 0 | W: 0 | N: 2
## ✔ manymome 0.2.4 ── E: 0 | W: 0 | N: 0
## ✔ marginaleffects 0.24.0 ── E: 0 | W: 0 | N: 0
## ✔ MatchThem 1.2.1 ── E: 0 | W: 0 | N: 0
## ✔ medflex 0.6.10 ── E: 0 | W: 0 | N: 0
## ✔ metavcov 2.1.5 ── E: 0 | W: 0 | N: 0
## ✔ mi4p 1.2 ── E: 0 | W: 0 | N: 0
## ✔ micd 1.1.1 ── E: 0 | W: 0 | N: 0
## ✔ miceadds 3.17.44 ── E: 0 | W: 0 | N: 2
## ✔ miceafter 0.5.0 ── E: 0 | W: 0 | N: 0
## ✔ miceFast 0.8.2 ── E: 0 | W: 0 | N: 2
## ✔ micemd 1.10.0 ── E: 0 | W: 0 | N: 0
## ✔ microeco 1.10.0 ── E: 0 | W: 0 | N: 0
## ✔ midastouch 1.3 ── E: 0 | W: 0 | N: 1
## ✔ midfieldr 1.0.2 ── E: 1 | W: 0 | N: 1
## ✔ midoc 1.0.0 ── E: 0 | W: 0 | N: 0
## ✔ mifa 0.2.0 ── E: 0 | W: 0 | N: 1
## ✔ MIIPW 0.1.1 ── E: 0 | W: 0 | N: 0
## ✔ misaem 1.0.1 ── E: 0 | W: 0 | N: 0
## ✔ miselect 0.9.2 ── E: 0 | W: 0 | N: 0
## ✔ missCompare 1.0.3 ── E: 0 | W: 0 | N: 0
## ✔ missDiag 1.0.1 ── E: 0 | W: 0 | N: 0
## ✔ missMDA 1.19 ── E: 0 | W: 0 | N: 0
## ✔ misty 0.6.8 ── E: 0 | W: 0 | N: 0
## ✔ mitml 0.4.5 ── E: 0 | W: 0 | N: 0
## ✔ miWQS 0.4.4 ── E: 0 | W: 0 | N: 0
## ✔ mixgb 1.0.2 ── E: 0 | W: 0 | N: 0
## ✔ MixtureMissing 3.0.3 ── E: 0 | W: 0 | N: 0
## ✔ MKinfer 1.2 ── E: 0 | W: 0 | N: 0
## ✔ mlim 0.3.0 ── E: 0 | W: 0 | N: 1
## ✔ modelsummary 2.2.0 ── E: 0 | W: 0 | N: 0
## ✔ monoClust 1.2.1 ── E: 0 | W: 0 | N: 1
## ✔ MRPC 3.1.0 ── E: 0 | W: 0 | N: 0
## ✔ MSiP 1.3.7 ── E: 0 | W: 0 | N: 1
## ✔ mvnimpute 1.0.1 ── E: 0 | W: 0 | N: 0
## ✔ mvs 2.0.0 ── E: 0 | W: 0 | N: 0
## ✔ NIMAA 0.2.1 ── E: 0 | W: 0 | N: 2
## ✔ 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 0.24.0 ── 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
## ✔ qgcomp 2.15.2 ── E: 0 | W: 0 | N: 1
## ✔ Qtools 1.5.9 ── E: 0 | W: 0 | N: 0
## ✔ rattle 5.5.1 ── E: 0 | W: 0 | N: 3
## ✔ RBtest 1.1 ── E: 0 | W: 0 | N: 1
## ✔ realTimeloads 1.0.0 ── E: 1 | W: 0 | N: 0
## ✔ RefBasedMI 0.2.0 ── E: 0 | W: 0 | N: 0
## ✔ regmedint 1.0.1 ── E: 0 | W: 0 | N: 1
## ✔ rexposome 1.28.0 ── E: 0 | W: 5 | N: 4
## ✔ RfEmpImp 2.1.8 ── E: 0 | W: 0 | N: 0
## ✔ rms 6.8.2 ── E: 0 | W: 0 | N: 0
## I rmsb 1.1.1 ── E: 1 | W: 0 | N: 1
## ✔ RNAseqCovarImpute 1.4.0 ── E: 0 | W: 0 | N: 2
## ✔ rqlm 2.1.1 ── E: 0 | W: 0 | N: 0
## ✔ RSquaredMI 0.1.1 ── E: 0 | W: 0 | N: 0
## ✔ semmcci 1.1.4 ── E: 0 | W: 0 | N: 0
## ✔ semTools 0.5.6 ── E: 0 | W: 0 | N: 1
## ✔ seqimpute 2.1.0 ── E: 0 | W: 0 | N: 0
## ✔ shapeNA 0.0.2 ── E: 0 | W: 0 | N: 3
## ✔ sjmisc 2.8.10 ── E: 0 | W: 0 | N: 0
## ✔ smdi 0.3.1 ── E: 1 | W: 0 | N: 0
## ✔ sociome 2.2.5 ── E: 0 | W: 0 | N: 0
## ✔ StackImpute 0.1.0 ── E: 0 | W: 0 | N: 2
## ✔ superMICE 1.1.1 ── E: 0 | W: 0 | N: 1
## ✔ svyweight 0.1.0 ── E: 0 | W: 0 | N: 1
## ✔ SynDI 0.1.0 ── E: 0 | W: 0 | N: 2
## ✔ synergyfinder 3.14.0 ── E: 0 | W: 1 | N: 3
## ✔ TestDataImputation 2.3 ── E: 0 | W: 0 | N: 0
## ✔ tidySEM 0.2.7 ── E: 0 | W: 0 | N: 0
## ✔ vsmi 0.1.0 ── E: 0 | W: 0 | N: 0
## ✔ weights 1.0.4 ── E: 0 | W: 0 | N: 0
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 1 new problems
- We failed to check 3 packages
Issues with CRAN packages are summarised below.
(This reports the first line of each new failure)
- 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//RtmpM38C1S/filee1cf761be8f7’
- brms (NA)
- dynr (NA)
- rmsb (NA)
mice developer comment: These failures are unrelated to mice
See https://github.com/amices/mice/tree/master/revdep for additional details.