cran-comments.md
In stefvanbuuren/mice: Multivariate Imputation by Chained Equations
cran-comments
mice 3.16.0
Overview
This submission
- is a third resubmission, using
devtools::check(env_vars = c('_R_CHECK_DEPENDS_ONLY_' = "true")) to
mimmick CRAN incoming checks
- is a second resubmission, with
\donttest changed in \dontrun to
evade _R_CHECK_DEPENDS_ONLY_=true errors;
- is a resubmission of
mice 3.16.0 after the orphaned ucminf CRAN
package got a new maintainer;
- is tested with the
_R_CHECK_DEPENDS_ONLY_=true flag, as requested;
- solves the problems at
https://cran.r-project.org/web/checks/check_results_mice.html;
- contains new features and bug fixes, as described in the
NEWS.md.
Test environments
R.Version()
## $platform
## [1] "aarch64-apple-darwin20"
##
## $arch
## [1] "aarch64"
##
## $os
## [1] "darwin20"
##
## $system
## [1] "aarch64, darwin20"
##
## $status
## [1] ""
##
## $major
## [1] "4"
##
## $minor
## [1] "3.0"
##
## $year
## [1] "2023"
##
## $month
## [1] "04"
##
## $day
## [1] "21"
##
## $`svn rev`
## [1] "84292"
##
## $language
## [1] "R"
##
## $version.string
## [1] "R version 4.3.0 (2023-04-21)"
##
## $nickname
## [1] "Already Tomorrow"
Checks
win-builder
devtools::check_win_devel()
Status: OK
Rhub
devtools::check_rhub()
Windows
── mice 3.16.0: NOTE
Build ID: mice_3.16.0.tar.gz-018f40fa4cdc492d8c9f43b7e5f5e0e7
Platform: Windows Server 2022, R-devel, 64 bit
Submitted: 11m 27s ago
Build time: 11m 25s
❯ checking HTML version of manual ... [27s] NOTE
Skipping checking math rendering: package 'V8' unavailable
❯ checking for non-standard things in the check directory ... NOTE
Found the following files/directories:
''NULL''
❯ checking for detritus in the temp directory ... NOTE
Found the following files/directories:
'lastMiKTeXException'
0 errors ✔ | 0 warnings ✔ | 3 notes ✖
I believe these NOTES are benign.
Fedora Linux
Status: succes
Ubuntu 20.04
Status: succes
Debian
FAILURE
Running `R CMD build`...
* checking for file ‘/tmp/Rtmp5Lhzhn/remotes13171d81356/mice/DESCRIPTION’ ... OK
* preparing ‘mice’:
* checking DESCRIPTION meta-information ... OK
* cleaning src
* checking for LF line-endings in source and make files and shell scripts
* checking for empty or unneeded directories
* building ‘mice_3.16.0.tar.gz’
Installing package into ‘/home/docker/R’
(as ‘lib’ is unspecified)
Error : Bioconductor does not yet build and check packages for R version 4.4; see
https://bioconductor.org/install
ERROR: dependency ‘mitml’ is not available for package ‘mice’
* removing ‘/home/docker/R/mice’
> There were 20 warnings (use warnings() to see them)
>
Error : Bioconductor does not yet build and check packages for R version 4.4; see
https://bioconductor.org/install
> library(mice)
Error in library(mice) : there is no package called ‘mice’
Execution halted
Build step 'Execute shell' marked build as failure
Pinging https://builder.r-hub.io/build/FAILURE/mice_3.16.0.tar.gz-82dc7cda08814b25ac48be4b5c9c940b/2023-06-01T11:37:52Z
{"status":"ok"}
Finished: FAILURE
I believe I cannot do something to make this problem disappear.
Local checks
Package built by
library("devtools")
build()
R CMD CHECK mice_3.16.0.tar.gz
Status: OK
Local check using _R_CHECK_DEPENDS_ONLY_=true flag.
NOTE: Run in OSX terminal, not in Rstudio terminal.
env _R_CHECK_DEPENDS_ONLY_=true R CMD check mice_3.16.0.tar.gz
Status: OK
devtools::check(env_vars = c('_R_CHECK_DEPENDS_ONLY_' = "true"))
...
Status: OK
── R CMD check results ─────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────── mice 3.16.0 ────
Duration: 1m 13s
0 errors ✔ | 0 warnings ✔ | 0 notes ✔
Downstream dependencies
Overview
mice has 114 downstream dependencies
# NOTE: Temporarily remove credentials line from .Rprofile
library(revdepcheck)
revdep_reset()
revdep_check(pkg = ".", num_workers = 10, quiet = FALSE)
revdepcheck::revdep_summary()
## ✔ accelmissing 1.4 ── E: 0 | W: 0 | N: 0
## ✔ adjustedCurves 0.10.1 ── E: 0 | W: 0 | N: 0
## ✔ alookr 0.3.7 ── E: 0 | W: 0 | N: 0
## ✔ autoReg 0.3.2 ── E: 0 | W: 0 | N: 0
## ✔ BaM 1.0.3 ── E: 0 | W: 0 | N: 0
## ✔ basecamb 1.1.2 ── E: 0 | W: 0 | N: 0
## ✔ BGGM 2.0.4 ── E: 0 | W: 0 | N: 2
## ✔ binaryTimeSeries 1.0.2 ── E: 0 | W: 0 | N: 0
## ✔ biokNN 0.1.0 ── E: 0 | W: 0 | N: 1
## ✖ bipd 0.3 ── E: 0 | W: 0 | N: 0-1+1
## ✔ bootImpute 1.2.0 ── E: 0 | W: 0 | N: 0
## ✔ brms 2.19.0 ── E: 0 | W: 0 | N: 2
## ✔ brokenstick 2.5.0 ── E: 0 | W: 0 | N: 0
## ✔ broom.helpers 1.13.0 ── E: 0 | W: 0 | N: 0
## ✔ bucky 1.0.7 ── E: 0 | W: 0 | N: 2
## ✔ CALIBERrfimpute 1.0.7 ── E: 0 | W: 0 | N: 0
## ✔ cati 0.99.4 ── E: 0 | W: 0 | N: 0
## ✔ censcyt 1.8.0 ── E: 0 | W: 0 | N: 2
## ✔ cobalt 4.5.1 ── E: 0 | W: 0 | N: 0
## ✔ dlookr 0.6.1 ── E: 0 | W: 0 | N: 0
## I dynr 0.1.16.91 ── E: 1 | W: 0 | N: 0
## ✔ eatRep 0.14.7 ── E: 0 | W: 0 | N: 0
## ✔ finalfit 1.0.6 ── E: 0 | W: 0 | N: 2
## ✔ FLAME 2.1.1 ── 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 1.2.2 ── E: 0 | W: 0 | N: 0
## ✔ ggmice 0.0.1 ── E: 0 | W: 0 | N: 0
## ✔ gtsummary 1.7.1 ── E: 0 | W: 0 | N: 0
## ✔ HardyWeinberg 1.7.5 ── E: 0 | W: 0 | N: 1
## ✔ hhsmm 0.3.5 ── E: 0 | W: 0 | N: 0
## ✔ Hmisc 5.1.0 ── E: 0 | W: 0 | N: 1
## ✔ holodeck 0.2.1 ── E: 0 | W: 0 | N: 1
## ✔ hot.deck 1.2 ── E: 0 | W: 0 | N: 0
## ✔ howManyImputations 0.2.4 ── E: 0 | W: 0 | N: 0
## ✔ HSAUR3 1.0.14 ── E: 0 | W: 0 | N: 0
## I idem 5.1 ── E: 1 | W: 0 | N: 0
## ✔ ImputeRobust 1.3.1 ── E: 0 | W: 0 | N: 0
## ✔ insight 0.19.2 ── E: 0 | W: 0 | N: 1
## ✔ intmed 0.1.2 ── E: 0 | W: 0 | N: 0
## ✔ IPWboxplot 0.1.1 ── E: 0 | W: 0 | N: 0
## ✔ JWileymisc 1.4.0 ── E: 0 | W: 0 | N: 0
## ✔ konfound 0.4.0 ── E: 0 | W: 0 | N: 1
## ✔ lavaan.survey 1.1.3.1 ── E: 1 | W: 0 | N: 0
## ✔ LMMstar 0.9.0 ── E: 0 | W: 0 | N: 1
## ✔ logistf 1.25.0 ── E: 0 | W: 0 | N: 0
## ✔ LSAmitR 1.0.3 ── E: 0 | W: 0 | N: 2
## ✔ manydata 0.8.2 ── E: 0 | W: 0 | N: 1
## ✔ marginaleffects 0.12.0 ── E: 0 | W: 0 | N: 1
## ✖ MatchThem 1.0.1 ── E: 0 | W: 0 +1 | N: 0
## ✔ mdapack 0.0.2 ── E: 0 | W: 0 | N: 2
## ✔ medflex 0.6.7 ── E: 1 | W: 1 | N: 0
## ✔ metavcov 2.1.4 ── E: 0 | W: 0 | N: 0
## ✔ mi4p 1.1 ── E: 0 | W: 0 | N: 0
## ✔ micd 1.1.1 ── E: 0 | W: 0 | N: 0
## ✔ miceadds 3.16.18 ── E: 0 | W: 0 | N: 3
## ✔ miceafter 0.5.0 ── E: 0 | W: 0 | N: 0
## ✔ miceFast 0.8.2 ── E: 0 | W: 0 | N: 1
## ✔ micemd 1.8.0 ── E: 0 | W: 0 | N: 1
## ✔ microeco 0.19.0 ── E: 0 | W: 0 | N: 0
## ✔ midastouch 1.3 ── E: 0 | W: 0 | N: 1
## ✔ 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 0.9.0 ── 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 1.18 ── 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 2.0.0 ── E: 0 | W: 0 | N: 0
## ✔ MKinfer 1.1 ── E: 0 | W: 0 | N: 0
## ✔ mlim 0.3.0 ── E: 0 | W: 0 | N: 0
## ✔ modelsummary 1.4.1 ── E: 0 | W: 0 | N: 0
## ✔ monoClust 1.2.1 ── E: 0 | W: 0 | N: 0
## ✔ 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
## ✔ NADIA 0.4.2 ── E: 0 | W: 0 | N: 1
## ✔ NIMAA 0.2.1 ── E: 0 | W: 0 | N: 2
## ✔ nncc 1.0.1 ── E: 0 | W: 0 | N: 0
## ✔ ordbetareg 0.7.1 ── E: 0 | W: 0 | N: 2
## ✔ OTrecod 0.1.2 ── E: 0 | W: 0 | N: 0
## ✔ parameters 0.21.1 ── E: 0 | W: 0 | N: 1
## ✔ pema 0.1.3 ── E: 0 | W: 0 | N: 2
## I pguIMP 0.0.0.3 ── E: 1 | W: 0 | N: 0
## ✖ pre 1.0.6 ── E: 0 +1 | W: 0 | N: 0
## ✔ psfmi 1.1.0 ── E: 0 | W: 0 | N: 0
## ✔ qgcomp 2.10.1 ── E: 0 | W: 0 | N: 0
## ✔ Qtools 1.5.6 ── 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
## ✔ RefBasedMI 0.1.0 ── E: 0 | W: 0 | N: 0
## ✔ regmedint 1.0.0 ── E: 0 | W: 0 | N: 1
## ✔ RegularizedSCA 0.5.4 ── E: 0 | W: 0 | N: 0
## I Replication 0.1.2 ── E: 1 | W: 0 | N: 0
## ✔ rexposome 1.22.0 ── E: 1 | W: 5 | N: 2
## ✔ RfEmpImp 2.1.8 ── E: 0 | W: 0 | N: 0
## ✔ rms 6.7.0 ── E: 0 | W: 0 | N: 0
## ✔ rmsb 0.1.0 ── E: 0 | W: 0 | N: 3
## ✔ semTools 0.5.6 ── E: 0 | W: 0 | N: 0
## ✔ seqimpute 1.8 ── E: 0 | W: 0 | N: 0
## ✔ shapeNA 0.0.2 ── E: 0 | W: 0 | N: 2
## ✔ sjmisc 2.8.9 ── E: 0 | W: 0 | N: 0
## ✔ SLOPE 0.5.0 ── E: 0 | W: 0 | N: 2
## ✔ sociome 2.2.1 ── E: 0 | W: 0 | N: 0
## ✔ StackImpute 0.1.0 ── E: 0 | W: 0 | N: 1
## ✔ superMICE 1.1.1 ── E: 0 | W: 0 | N: 1
## ✔ svyweight 0.1.0 ── E: 0 | W: 0 | N: 0
## ✔ SynDI 0.1.0 ── E: 0 | W: 0 | N: 1
## ✔ synergyfinder 3.8.2 ── E: 0 | W: 1 | N: 3
## ✔ TestDataImputation 2.3 ── E: 0 | W: 0 | N: 0
## ✔ weights 1.0.4 ── E: 0 | W: 0 | N: 0
New issues
MatchThem
There is one new warning, for the MatchThem package:
revdepcheck::revdep_details(revdep = "MatchThem")
## ══ Reverse dependency check ═════════════════════════════════ MatchThem 1.0.1 ══
##
## Status: BROKEN
##
## ── Newly failing
##
## ✖ checking Rd cross-references ... WARNING
##
## ── Before ──────────────────────────────────────────────────────────────────────
## 0 errors ✔ | 0 warnings ✔ | 0 notes ✔
##
## ── After ───────────────────────────────────────────────────────────────────────
## ❯ checking Rd cross-references ... WARNING
## Missing link or links in documentation object 'cbind.Rd':
## ‘[mice:cbind.mids]{mice::cbind.mids}’
##
## See section 'Cross-references' in the 'Writing R Extensions' manual.
##
## 0 errors ✔ | 1 warning ✖ | 0 notes ✔
- I alerted the maintainer of the
MatchThem package that the
documentation for cbind.mids() was removed from the mice package
to conform to CRAN guidelines. The maintainer responded this will be
fixed in the next release.
bipd
revdepcheck::revdep_details(revdep = "bipd")
## ══ Reverse dependency check ════════════════════════════════════════ bipd 0.3 ══
##
## Status: BROKEN
##
## ── Fixed
##
## ✔ checking dependencies in R code ...sh: line 1: 64022 Segmentation fault: 11 R_DEFAULT_PACKAGES=NULL '/Library/Frameworks/R.framework/Resources/bin/R' --vanilla --no-echo 2>&1 < '/var/folders/5_/g85d42yj50b6lrjq4rzjzg8w0000gn/T//RtmpPAGHHl/filef76c784da58a'
##
## ── Newly failing
##
## ✖ checking dependencies in R code ...sh: line 1: 64105 Segmentation fault: 11 R_DEFAULT_PACKAGES=NULL '/Library/Frameworks/R.framework/Resources/bin/R' --vanilla --no-echo 2>&1 < '/var/folders/5_/g85d42yj50b6lrjq4rzjzg8w0000gn/T//RtmpcESnnw/filef7d530e954ed'
##
## ── Before ──────────────────────────────────────────────────────────────────────
## ❯ checking dependencies in R code ...sh: line 1: 64022 Segmentation fault: 11 R_DEFAULT_PACKAGES=NULL '/Library/Frameworks/R.framework/Resources/bin/R' --vanilla --no-echo 2>&1 < '/var/folders/5_/g85d42yj50b6lrjq4rzjzg8w0000gn/T//RtmpPAGHHl/filef76c784da58a'
## NOTE
##
## *** caught segfault ***
## address 0x6c65432f6c61636f, cause 'invalid permissions'
##
## Traceback:
## 1: dyn.load(file, DLLpath = DLLpath, ...)
## 2: library.dynam(lib, package, package.lib)
## 3: loadNamespace(j <- i[[1L]], c(lib.loc, .libPaths()), versionCheck = vI[[j]])
## 4: asNamespace(ns)
## 5: namespaceImportFrom(ns, loadNamespace(j <- i[[1L]], c(lib.loc, .libPaths()), versionCheck = vI[[j]]), i[[2L]], from = package)
## 6: loadNamespace(p)
## 7: withCallingHandlers(expr, message = function(c) if (inherits(c, classes)) tryInvokeRestart("muffleMessage"))
## 8: suppressMessages(loadNamespace(p))
## 9: withCallingHandlers(expr, warning = function(w) if (inherits(w, classes)) tryInvokeRestart("muffleWarning"))
## 10: suppressWarnings(suppressMessages(loadNamespace(p)))
## 11: doTryCatch(return(expr), name, parentenv, handler)
## 12: tryCatchOne(expr, names, parentenv, handlers[[1L]])
## 13: tryCatchList(expr, classes, parentenv, handlers)
## 14: tryCatch(suppressWarnings(suppressMessages(loadNamespace(p))), error = function(e) e)
## 15: tools:::.check_packages_used(package = "bipd")
## An irrecoverable exception occurred. R is aborting now ...
##
## 0 errors ✔ | 0 warnings ✔ | 1 note ✖
##
## ── After ───────────────────────────────────────────────────────────────────────
## ❯ checking dependencies in R code ...sh: line 1: 64105 Segmentation fault: 11 R_DEFAULT_PACKAGES=NULL '/Library/Frameworks/R.framework/Resources/bin/R' --vanilla --no-echo 2>&1 < '/var/folders/5_/g85d42yj50b6lrjq4rzjzg8w0000gn/T//RtmpcESnnw/filef7d530e954ed'
## NOTE
##
## *** caught segfault ***
## address 0x6c65432f6c61636f, cause 'invalid permissions'
##
## Traceback:
## 1: dyn.load(file, DLLpath = DLLpath, ...)
## 2: library.dynam(lib, package, package.lib)
## 3: loadNamespace(j <- i[[1L]], c(lib.loc, .libPaths()), versionCheck = vI[[j]])
## 4: asNamespace(ns)
## 5: namespaceImportFrom(ns, loadNamespace(j <- i[[1L]], c(lib.loc, .libPaths()), versionCheck = vI[[j]]), i[[2L]], from = package)
## 6: loadNamespace(p)
## 7: withCallingHandlers(expr, message = function(c) if (inherits(c, classes)) tryInvokeRestart("muffleMessage"))
## 8: suppressMessages(loadNamespace(p))
## 9: withCallingHandlers(expr, warning = function(w) if (inherits(w, classes)) tryInvokeRestart("muffleWarning"))
## 10: suppressWarnings(suppressMessages(loadNamespace(p)))
## 11: doTryCatch(return(expr), name, parentenv, handler)
## 12: tryCatchOne(expr, names, parentenv, handlers[[1L]])
## 13: tryCatchList(expr, classes, parentenv, handlers)
## 14: tryCatch(suppressWarnings(suppressMessages(loadNamespace(p))), error = function(e) e)
## 15: tools:::.check_packages_used(package = "bipd")
## An irrecoverable exception occurred. R is aborting now ...
##
## 0 errors ✔ | 0 warnings ✔ | 1 note ✖
- The novel NOTE for
bipd is equivalent to the old one. I contacted
the maintainer previously. Did not repeat it now.
pre
- There is a new error generated by
test_pre_misc.R of the pre
package (mice is on pre Suggests):
revdepcheck::revdep_details(revdep = "pre")
## ══ Reverse dependency check ═══════════════════════════════════════ pre 1.0.6 ══
##
## Status: BROKEN
##
## ── Newly failing
##
## ✖ checking tests ...
##
## ── Before ──────────────────────────────────────────────────────────────────────
## 0 errors ✔ | 0 warnings ✔ | 0 notes ✔
##
## ── After ───────────────────────────────────────────────────────────────────────
## ❯ checking tests ...
## See below...
##
## ── Test failures ───────────────────────────────────────────────── testthat ────
##
## > library(testthat)
## > library(pre)
## >
## > #####
## > # partykit and earth is loaded as failures of tests may be caused by the version
## > # of either package. Thus, we print the sessionInfo
## >
## > library(earth)
## Loading required package: Formula
## Loading required package: plotmo
## Loading required package: plotrix
## Loading required package: TeachingDemos
## > library(partykit)
## Loading required package: grid
## Loading required package: libcoin
## Loading required package: mvtnorm
## > print(sessionInfo())
## R version 4.3.0 (2023-04-21)
## Platform: aarch64-apple-darwin20 (64-bit)
## Running under: macOS Ventura 13.4
##
## Matrix products: default
## BLAS: /Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/lib/libRblas.0.dylib
## LAPACK: /Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/lib/libRlapack.dylib; LAPACK version 3.11.0
##
## locale:
## [1] C/en_US.UTF-8/en_US.UTF-8/C/en_US.UTF-8/en_US.UTF-8
##
## time zone: Europe/Amsterdam
## tzcode source: internal
##
## attached base packages:
## [1] grid stats graphics grDevices utils datasets methods
## [8] base
##
## other attached packages:
## [1] partykit_1.2-20 mvtnorm_1.1-3 libcoin_1.0-9 earth_5.3.2
## [5] plotmo_3.6.2 TeachingDemos_2.12 plotrix_3.8-2 Formula_1.2-5
## [9] pre_1.0.6 testthat_3.1.8
##
## loaded via a namespace (and not attached):
## [1] cli_3.6.1 rlang_1.1.1 stringi_1.7.12 MatrixModels_0.5-1
## [5] glue_1.6.2 glmnet_4.1-7 brio_1.1.3 lifecycle_1.0.3
## [9] foreach_1.5.2 stringr_1.5.0 compiler_4.3.0 codetools_0.2-19
## [13] Rcpp_1.0.10 lattice_0.21-8 R6_2.5.1 splines_4.3.0
## [17] inum_1.0-5 shape_1.4.6 magrittr_2.0.3 rpart_4.1.19
## [21] Matrix_1.5-4.1 tools_4.3.0 iterators_1.0.14 survival_3.5-5
## >
## > test_check("pre")
## [ FAIL 1 | WARN 0 | SKIP 0 | PASS 122 ]
##
## ══ Failed tests ════════════════════════════════════════════════════════════════
## ── Error ('test_pre_misc.R:94:3'): cvpre gives previous results with airquality data ──
## Error in `serverSocket(port = port)`: creation of server socket failed: port 11471 cannot be opened
## Backtrace:
## ▆
## 1. └─parallel::makeCluster(2L) at test_pre_misc.R:94:2
## 2. └─parallel::makePSOCKcluster(names = spec, ...)
## 3. └─base::serverSocket(port = port)
##
## [ FAIL 1 | WARN 0 | SKIP 0 | PASS 122 ]
## Error: Test failures
## Execution halted
##
## 1 error ✖ | 0 warnings ✔ | 0 notes ✔
- I tried reproducing the error but stopped my attempt due to the
complex structure of the testing script. I contacted the
pre
maintainer by means of issue
https://github.com/marjoleinF/pre/issues/30.
stefvanbuuren/mice documentation built on May 6, 2024, 12:17 p.m.
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cran-comments
mice 3.16.0
Overview
This submission
- is a third resubmission, using
devtools::check(env_vars = c('_R_CHECK_DEPENDS_ONLY_' = "true"))to mimmick CRAN incoming checks - is a second resubmission, with
\donttestchanged in\dontrunto evade_R_CHECK_DEPENDS_ONLY_=trueerrors; - is a resubmission of
mice 3.16.0after the orphaneducminfCRAN package got a new maintainer; - is tested with the
_R_CHECK_DEPENDS_ONLY_=trueflag, as requested; - solves the problems at
https://cran.r-project.org/web/checks/check_results_mice.html; - contains new features and bug fixes, as described in the
NEWS.md.
Test environments
R.Version()
## $platform
## [1] "aarch64-apple-darwin20"
##
## $arch
## [1] "aarch64"
##
## $os
## [1] "darwin20"
##
## $system
## [1] "aarch64, darwin20"
##
## $status
## [1] ""
##
## $major
## [1] "4"
##
## $minor
## [1] "3.0"
##
## $year
## [1] "2023"
##
## $month
## [1] "04"
##
## $day
## [1] "21"
##
## $`svn rev`
## [1] "84292"
##
## $language
## [1] "R"
##
## $version.string
## [1] "R version 4.3.0 (2023-04-21)"
##
## $nickname
## [1] "Already Tomorrow"
Checks
win-builder
devtools::check_win_devel()
Status: OK
Rhub
devtools::check_rhub()
Windows
── mice 3.16.0: NOTE
Build ID: mice_3.16.0.tar.gz-018f40fa4cdc492d8c9f43b7e5f5e0e7
Platform: Windows Server 2022, R-devel, 64 bit
Submitted: 11m 27s ago
Build time: 11m 25s
❯ checking HTML version of manual ... [27s] NOTE
Skipping checking math rendering: package 'V8' unavailable
❯ checking for non-standard things in the check directory ... NOTE
Found the following files/directories:
''NULL''
❯ checking for detritus in the temp directory ... NOTE
Found the following files/directories:
'lastMiKTeXException'
0 errors ✔ | 0 warnings ✔ | 3 notes ✖
I believe these NOTES are benign.
Fedora Linux
Status: succes
Ubuntu 20.04
Status: succes
Debian
FAILURE
Running `R CMD build`...
* checking for file ‘/tmp/Rtmp5Lhzhn/remotes13171d81356/mice/DESCRIPTION’ ... OK
* preparing ‘mice’:
* checking DESCRIPTION meta-information ... OK
* cleaning src
* checking for LF line-endings in source and make files and shell scripts
* checking for empty or unneeded directories
* building ‘mice_3.16.0.tar.gz’
Installing package into ‘/home/docker/R’
(as ‘lib’ is unspecified)
Error : Bioconductor does not yet build and check packages for R version 4.4; see
https://bioconductor.org/install
ERROR: dependency ‘mitml’ is not available for package ‘mice’
* removing ‘/home/docker/R/mice’
> There were 20 warnings (use warnings() to see them)
>
Error : Bioconductor does not yet build and check packages for R version 4.4; see
https://bioconductor.org/install
> library(mice)
Error in library(mice) : there is no package called ‘mice’
Execution halted
Build step 'Execute shell' marked build as failure
Pinging https://builder.r-hub.io/build/FAILURE/mice_3.16.0.tar.gz-82dc7cda08814b25ac48be4b5c9c940b/2023-06-01T11:37:52Z
{"status":"ok"}
Finished: FAILURE
I believe I cannot do something to make this problem disappear.
Local checks
Package built by
library("devtools")
build()
R CMD CHECK mice_3.16.0.tar.gz
Status: OK
Local check using _R_CHECK_DEPENDS_ONLY_=true flag.
NOTE: Run in OSX terminal, not in Rstudio terminal.
env _R_CHECK_DEPENDS_ONLY_=true R CMD check mice_3.16.0.tar.gz
Status: OK
devtools::check(env_vars = c('_R_CHECK_DEPENDS_ONLY_' = "true"))
...
Status: OK
── R CMD check results ─────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────── mice 3.16.0 ────
Duration: 1m 13s
0 errors ✔ | 0 warnings ✔ | 0 notes ✔
Downstream dependencies
Overview
mice has 114 downstream dependencies
# NOTE: Temporarily remove credentials line from .Rprofile
library(revdepcheck)
revdep_reset()
revdep_check(pkg = ".", num_workers = 10, quiet = FALSE)
revdepcheck::revdep_summary()
## ✔ accelmissing 1.4 ── E: 0 | W: 0 | N: 0
## ✔ adjustedCurves 0.10.1 ── E: 0 | W: 0 | N: 0
## ✔ alookr 0.3.7 ── E: 0 | W: 0 | N: 0
## ✔ autoReg 0.3.2 ── E: 0 | W: 0 | N: 0
## ✔ BaM 1.0.3 ── E: 0 | W: 0 | N: 0
## ✔ basecamb 1.1.2 ── E: 0 | W: 0 | N: 0
## ✔ BGGM 2.0.4 ── E: 0 | W: 0 | N: 2
## ✔ binaryTimeSeries 1.0.2 ── E: 0 | W: 0 | N: 0
## ✔ biokNN 0.1.0 ── E: 0 | W: 0 | N: 1
## ✖ bipd 0.3 ── E: 0 | W: 0 | N: 0-1+1
## ✔ bootImpute 1.2.0 ── E: 0 | W: 0 | N: 0
## ✔ brms 2.19.0 ── E: 0 | W: 0 | N: 2
## ✔ brokenstick 2.5.0 ── E: 0 | W: 0 | N: 0
## ✔ broom.helpers 1.13.0 ── E: 0 | W: 0 | N: 0
## ✔ bucky 1.0.7 ── E: 0 | W: 0 | N: 2
## ✔ CALIBERrfimpute 1.0.7 ── E: 0 | W: 0 | N: 0
## ✔ cati 0.99.4 ── E: 0 | W: 0 | N: 0
## ✔ censcyt 1.8.0 ── E: 0 | W: 0 | N: 2
## ✔ cobalt 4.5.1 ── E: 0 | W: 0 | N: 0
## ✔ dlookr 0.6.1 ── E: 0 | W: 0 | N: 0
## I dynr 0.1.16.91 ── E: 1 | W: 0 | N: 0
## ✔ eatRep 0.14.7 ── E: 0 | W: 0 | N: 0
## ✔ finalfit 1.0.6 ── E: 0 | W: 0 | N: 2
## ✔ FLAME 2.1.1 ── 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 1.2.2 ── E: 0 | W: 0 | N: 0
## ✔ ggmice 0.0.1 ── E: 0 | W: 0 | N: 0
## ✔ gtsummary 1.7.1 ── E: 0 | W: 0 | N: 0
## ✔ HardyWeinberg 1.7.5 ── E: 0 | W: 0 | N: 1
## ✔ hhsmm 0.3.5 ── E: 0 | W: 0 | N: 0
## ✔ Hmisc 5.1.0 ── E: 0 | W: 0 | N: 1
## ✔ holodeck 0.2.1 ── E: 0 | W: 0 | N: 1
## ✔ hot.deck 1.2 ── E: 0 | W: 0 | N: 0
## ✔ howManyImputations 0.2.4 ── E: 0 | W: 0 | N: 0
## ✔ HSAUR3 1.0.14 ── E: 0 | W: 0 | N: 0
## I idem 5.1 ── E: 1 | W: 0 | N: 0
## ✔ ImputeRobust 1.3.1 ── E: 0 | W: 0 | N: 0
## ✔ insight 0.19.2 ── E: 0 | W: 0 | N: 1
## ✔ intmed 0.1.2 ── E: 0 | W: 0 | N: 0
## ✔ IPWboxplot 0.1.1 ── E: 0 | W: 0 | N: 0
## ✔ JWileymisc 1.4.0 ── E: 0 | W: 0 | N: 0
## ✔ konfound 0.4.0 ── E: 0 | W: 0 | N: 1
## ✔ lavaan.survey 1.1.3.1 ── E: 1 | W: 0 | N: 0
## ✔ LMMstar 0.9.0 ── E: 0 | W: 0 | N: 1
## ✔ logistf 1.25.0 ── E: 0 | W: 0 | N: 0
## ✔ LSAmitR 1.0.3 ── E: 0 | W: 0 | N: 2
## ✔ manydata 0.8.2 ── E: 0 | W: 0 | N: 1
## ✔ marginaleffects 0.12.0 ── E: 0 | W: 0 | N: 1
## ✖ MatchThem 1.0.1 ── E: 0 | W: 0 +1 | N: 0
## ✔ mdapack 0.0.2 ── E: 0 | W: 0 | N: 2
## ✔ medflex 0.6.7 ── E: 1 | W: 1 | N: 0
## ✔ metavcov 2.1.4 ── E: 0 | W: 0 | N: 0
## ✔ mi4p 1.1 ── E: 0 | W: 0 | N: 0
## ✔ micd 1.1.1 ── E: 0 | W: 0 | N: 0
## ✔ miceadds 3.16.18 ── E: 0 | W: 0 | N: 3
## ✔ miceafter 0.5.0 ── E: 0 | W: 0 | N: 0
## ✔ miceFast 0.8.2 ── E: 0 | W: 0 | N: 1
## ✔ micemd 1.8.0 ── E: 0 | W: 0 | N: 1
## ✔ microeco 0.19.0 ── E: 0 | W: 0 | N: 0
## ✔ midastouch 1.3 ── E: 0 | W: 0 | N: 1
## ✔ 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 0.9.0 ── 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 1.18 ── 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 2.0.0 ── E: 0 | W: 0 | N: 0
## ✔ MKinfer 1.1 ── E: 0 | W: 0 | N: 0
## ✔ mlim 0.3.0 ── E: 0 | W: 0 | N: 0
## ✔ modelsummary 1.4.1 ── E: 0 | W: 0 | N: 0
## ✔ monoClust 1.2.1 ── E: 0 | W: 0 | N: 0
## ✔ 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
## ✔ NADIA 0.4.2 ── E: 0 | W: 0 | N: 1
## ✔ NIMAA 0.2.1 ── E: 0 | W: 0 | N: 2
## ✔ nncc 1.0.1 ── E: 0 | W: 0 | N: 0
## ✔ ordbetareg 0.7.1 ── E: 0 | W: 0 | N: 2
## ✔ OTrecod 0.1.2 ── E: 0 | W: 0 | N: 0
## ✔ parameters 0.21.1 ── E: 0 | W: 0 | N: 1
## ✔ pema 0.1.3 ── E: 0 | W: 0 | N: 2
## I pguIMP 0.0.0.3 ── E: 1 | W: 0 | N: 0
## ✖ pre 1.0.6 ── E: 0 +1 | W: 0 | N: 0
## ✔ psfmi 1.1.0 ── E: 0 | W: 0 | N: 0
## ✔ qgcomp 2.10.1 ── E: 0 | W: 0 | N: 0
## ✔ Qtools 1.5.6 ── 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
## ✔ RefBasedMI 0.1.0 ── E: 0 | W: 0 | N: 0
## ✔ regmedint 1.0.0 ── E: 0 | W: 0 | N: 1
## ✔ RegularizedSCA 0.5.4 ── E: 0 | W: 0 | N: 0
## I Replication 0.1.2 ── E: 1 | W: 0 | N: 0
## ✔ rexposome 1.22.0 ── E: 1 | W: 5 | N: 2
## ✔ RfEmpImp 2.1.8 ── E: 0 | W: 0 | N: 0
## ✔ rms 6.7.0 ── E: 0 | W: 0 | N: 0
## ✔ rmsb 0.1.0 ── E: 0 | W: 0 | N: 3
## ✔ semTools 0.5.6 ── E: 0 | W: 0 | N: 0
## ✔ seqimpute 1.8 ── E: 0 | W: 0 | N: 0
## ✔ shapeNA 0.0.2 ── E: 0 | W: 0 | N: 2
## ✔ sjmisc 2.8.9 ── E: 0 | W: 0 | N: 0
## ✔ SLOPE 0.5.0 ── E: 0 | W: 0 | N: 2
## ✔ sociome 2.2.1 ── E: 0 | W: 0 | N: 0
## ✔ StackImpute 0.1.0 ── E: 0 | W: 0 | N: 1
## ✔ superMICE 1.1.1 ── E: 0 | W: 0 | N: 1
## ✔ svyweight 0.1.0 ── E: 0 | W: 0 | N: 0
## ✔ SynDI 0.1.0 ── E: 0 | W: 0 | N: 1
## ✔ synergyfinder 3.8.2 ── E: 0 | W: 1 | N: 3
## ✔ TestDataImputation 2.3 ── E: 0 | W: 0 | N: 0
## ✔ weights 1.0.4 ── E: 0 | W: 0 | N: 0
New issues
MatchThem
There is one new warning, for the MatchThem package:
revdepcheck::revdep_details(revdep = "MatchThem")
## ══ Reverse dependency check ═════════════════════════════════ MatchThem 1.0.1 ══
##
## Status: BROKEN
##
## ── Newly failing
##
## ✖ checking Rd cross-references ... WARNING
##
## ── Before ──────────────────────────────────────────────────────────────────────
## 0 errors ✔ | 0 warnings ✔ | 0 notes ✔
##
## ── After ───────────────────────────────────────────────────────────────────────
## ❯ checking Rd cross-references ... WARNING
## Missing link or links in documentation object 'cbind.Rd':
## ‘[mice:cbind.mids]{mice::cbind.mids}’
##
## See section 'Cross-references' in the 'Writing R Extensions' manual.
##
## 0 errors ✔ | 1 warning ✖ | 0 notes ✔
- I alerted the maintainer of the
MatchThempackage that the documentation forcbind.mids()was removed from themicepackage to conform to CRAN guidelines. The maintainer responded this will be fixed in the next release.
bipd
revdepcheck::revdep_details(revdep = "bipd")
## ══ Reverse dependency check ════════════════════════════════════════ bipd 0.3 ══
##
## Status: BROKEN
##
## ── Fixed
##
## ✔ checking dependencies in R code ...sh: line 1: 64022 Segmentation fault: 11 R_DEFAULT_PACKAGES=NULL '/Library/Frameworks/R.framework/Resources/bin/R' --vanilla --no-echo 2>&1 < '/var/folders/5_/g85d42yj50b6lrjq4rzjzg8w0000gn/T//RtmpPAGHHl/filef76c784da58a'
##
## ── Newly failing
##
## ✖ checking dependencies in R code ...sh: line 1: 64105 Segmentation fault: 11 R_DEFAULT_PACKAGES=NULL '/Library/Frameworks/R.framework/Resources/bin/R' --vanilla --no-echo 2>&1 < '/var/folders/5_/g85d42yj50b6lrjq4rzjzg8w0000gn/T//RtmpcESnnw/filef7d530e954ed'
##
## ── Before ──────────────────────────────────────────────────────────────────────
## ❯ checking dependencies in R code ...sh: line 1: 64022 Segmentation fault: 11 R_DEFAULT_PACKAGES=NULL '/Library/Frameworks/R.framework/Resources/bin/R' --vanilla --no-echo 2>&1 < '/var/folders/5_/g85d42yj50b6lrjq4rzjzg8w0000gn/T//RtmpPAGHHl/filef76c784da58a'
## NOTE
##
## *** caught segfault ***
## address 0x6c65432f6c61636f, cause 'invalid permissions'
##
## Traceback:
## 1: dyn.load(file, DLLpath = DLLpath, ...)
## 2: library.dynam(lib, package, package.lib)
## 3: loadNamespace(j <- i[[1L]], c(lib.loc, .libPaths()), versionCheck = vI[[j]])
## 4: asNamespace(ns)
## 5: namespaceImportFrom(ns, loadNamespace(j <- i[[1L]], c(lib.loc, .libPaths()), versionCheck = vI[[j]]), i[[2L]], from = package)
## 6: loadNamespace(p)
## 7: withCallingHandlers(expr, message = function(c) if (inherits(c, classes)) tryInvokeRestart("muffleMessage"))
## 8: suppressMessages(loadNamespace(p))
## 9: withCallingHandlers(expr, warning = function(w) if (inherits(w, classes)) tryInvokeRestart("muffleWarning"))
## 10: suppressWarnings(suppressMessages(loadNamespace(p)))
## 11: doTryCatch(return(expr), name, parentenv, handler)
## 12: tryCatchOne(expr, names, parentenv, handlers[[1L]])
## 13: tryCatchList(expr, classes, parentenv, handlers)
## 14: tryCatch(suppressWarnings(suppressMessages(loadNamespace(p))), error = function(e) e)
## 15: tools:::.check_packages_used(package = "bipd")
## An irrecoverable exception occurred. R is aborting now ...
##
## 0 errors ✔ | 0 warnings ✔ | 1 note ✖
##
## ── After ───────────────────────────────────────────────────────────────────────
## ❯ checking dependencies in R code ...sh: line 1: 64105 Segmentation fault: 11 R_DEFAULT_PACKAGES=NULL '/Library/Frameworks/R.framework/Resources/bin/R' --vanilla --no-echo 2>&1 < '/var/folders/5_/g85d42yj50b6lrjq4rzjzg8w0000gn/T//RtmpcESnnw/filef7d530e954ed'
## NOTE
##
## *** caught segfault ***
## address 0x6c65432f6c61636f, cause 'invalid permissions'
##
## Traceback:
## 1: dyn.load(file, DLLpath = DLLpath, ...)
## 2: library.dynam(lib, package, package.lib)
## 3: loadNamespace(j <- i[[1L]], c(lib.loc, .libPaths()), versionCheck = vI[[j]])
## 4: asNamespace(ns)
## 5: namespaceImportFrom(ns, loadNamespace(j <- i[[1L]], c(lib.loc, .libPaths()), versionCheck = vI[[j]]), i[[2L]], from = package)
## 6: loadNamespace(p)
## 7: withCallingHandlers(expr, message = function(c) if (inherits(c, classes)) tryInvokeRestart("muffleMessage"))
## 8: suppressMessages(loadNamespace(p))
## 9: withCallingHandlers(expr, warning = function(w) if (inherits(w, classes)) tryInvokeRestart("muffleWarning"))
## 10: suppressWarnings(suppressMessages(loadNamespace(p)))
## 11: doTryCatch(return(expr), name, parentenv, handler)
## 12: tryCatchOne(expr, names, parentenv, handlers[[1L]])
## 13: tryCatchList(expr, classes, parentenv, handlers)
## 14: tryCatch(suppressWarnings(suppressMessages(loadNamespace(p))), error = function(e) e)
## 15: tools:::.check_packages_used(package = "bipd")
## An irrecoverable exception occurred. R is aborting now ...
##
## 0 errors ✔ | 0 warnings ✔ | 1 note ✖
- The novel NOTE for
bipdis equivalent to the old one. I contacted the maintainer previously. Did not repeat it now.
pre
- There is a new error generated by
test_pre_misc.Rof theprepackage (miceis onpreSuggests):
revdepcheck::revdep_details(revdep = "pre")
## ══ Reverse dependency check ═══════════════════════════════════════ pre 1.0.6 ══
##
## Status: BROKEN
##
## ── Newly failing
##
## ✖ checking tests ...
##
## ── Before ──────────────────────────────────────────────────────────────────────
## 0 errors ✔ | 0 warnings ✔ | 0 notes ✔
##
## ── After ───────────────────────────────────────────────────────────────────────
## ❯ checking tests ...
## See below...
##
## ── Test failures ───────────────────────────────────────────────── testthat ────
##
## > library(testthat)
## > library(pre)
## >
## > #####
## > # partykit and earth is loaded as failures of tests may be caused by the version
## > # of either package. Thus, we print the sessionInfo
## >
## > library(earth)
## Loading required package: Formula
## Loading required package: plotmo
## Loading required package: plotrix
## Loading required package: TeachingDemos
## > library(partykit)
## Loading required package: grid
## Loading required package: libcoin
## Loading required package: mvtnorm
## > print(sessionInfo())
## R version 4.3.0 (2023-04-21)
## Platform: aarch64-apple-darwin20 (64-bit)
## Running under: macOS Ventura 13.4
##
## Matrix products: default
## BLAS: /Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/lib/libRblas.0.dylib
## LAPACK: /Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/lib/libRlapack.dylib; LAPACK version 3.11.0
##
## locale:
## [1] C/en_US.UTF-8/en_US.UTF-8/C/en_US.UTF-8/en_US.UTF-8
##
## time zone: Europe/Amsterdam
## tzcode source: internal
##
## attached base packages:
## [1] grid stats graphics grDevices utils datasets methods
## [8] base
##
## other attached packages:
## [1] partykit_1.2-20 mvtnorm_1.1-3 libcoin_1.0-9 earth_5.3.2
## [5] plotmo_3.6.2 TeachingDemos_2.12 plotrix_3.8-2 Formula_1.2-5
## [9] pre_1.0.6 testthat_3.1.8
##
## loaded via a namespace (and not attached):
## [1] cli_3.6.1 rlang_1.1.1 stringi_1.7.12 MatrixModels_0.5-1
## [5] glue_1.6.2 glmnet_4.1-7 brio_1.1.3 lifecycle_1.0.3
## [9] foreach_1.5.2 stringr_1.5.0 compiler_4.3.0 codetools_0.2-19
## [13] Rcpp_1.0.10 lattice_0.21-8 R6_2.5.1 splines_4.3.0
## [17] inum_1.0-5 shape_1.4.6 magrittr_2.0.3 rpart_4.1.19
## [21] Matrix_1.5-4.1 tools_4.3.0 iterators_1.0.14 survival_3.5-5
## >
## > test_check("pre")
## [ FAIL 1 | WARN 0 | SKIP 0 | PASS 122 ]
##
## ══ Failed tests ════════════════════════════════════════════════════════════════
## ── Error ('test_pre_misc.R:94:3'): cvpre gives previous results with airquality data ──
## Error in `serverSocket(port = port)`: creation of server socket failed: port 11471 cannot be opened
## Backtrace:
## ▆
## 1. └─parallel::makeCluster(2L) at test_pre_misc.R:94:2
## 2. └─parallel::makePSOCKcluster(names = spec, ...)
## 3. └─base::serverSocket(port = port)
##
## [ FAIL 1 | WARN 0 | SKIP 0 | PASS 122 ]
## Error: Test failures
## Execution halted
##
## 1 error ✖ | 0 warnings ✔ | 0 notes ✔
- I tried reproducing the error but stopped my attempt due to the
complex structure of the testing script. I contacted the
premaintainer by means of issue https://github.com/marjoleinF/pre/issues/30.
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