This submission
devtools::check(env_vars = c('_R_CHECK_DEPENDS_ONLY_' = "true"))
to
mimmick CRAN incoming checks\donttest
changed in \dontrun
to
evade _R_CHECK_DEPENDS_ONLY_=true
errors;mice 3.16.0
after the orphaned ucminf
CRAN
package got a new maintainer;_R_CHECK_DEPENDS_ONLY_=true
flag, as requested;https://cran.r-project.org/web/checks/check_results_mice.html
;NEWS.md
.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"
devtools::check_win_devel()
Status: OK
devtools::check_rhub()
── 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.
Status: succes
Status: succes
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.
Package built by
library("devtools")
build()
R CMD CHECK mice_3.16.0.tar.gz
Status: OK
_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 ✔
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
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 ✔
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 ✖
bipd
is equivalent to the old one. I contacted
the maintainer previously. Did not repeat it now.pre
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 ✔
pre
maintainer by means of issue
https://github.com/marjoleinF/pre/issues/30.Add the following code to your website.
For more information on customizing the embed code, read Embedding Snippets.