In stefvanbuuren/mice: Multivariate Imputation by Chained Equations

knitr::opts_chunk$set(echo = TRUE)

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()

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()

```{bash eval=FALSE} 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.

```{bash eval=FALSE}
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()

New issues

MatchThem

There is one new warning, for the MatchThem package:

revdepcheck::revdep_details(revdep = "MatchThem")

• 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")

• 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")

• 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.