From da18a23424eb0f47bfc1d4c051eb510595f2ae22 Mon Sep 17 00:00:00 2001 From: Stef van Buuren Date: Thu, 14 May 2020 16:30:02 +0200 Subject: [PATCH] Update cran-comments --- cran-comments.Rmd | 107 +++++++++-- cran-comments.md | 443 +++++++++++++++++++--------------------------- 2 files changed, 275 insertions(+), 275 deletions(-) diff --git a/cran-comments.Rmd b/cran-comments.Rmd index a4b7dcd0c..c0c347a73 100644 --- a/cran-comments.Rmd +++ b/cran-comments.Rmd @@ -13,7 +13,13 @@ knitr::opts_chunk$set(echo = TRUE) This update `mice 3.9.0` adds new functionality, reduces dependencies and provides solutions for issues found in `mice 3.8.0` and before. -## Checks +## Test environments + +* local OS X install, 10.15.4, R 4.0.0 +* win-builder +* Rhub + +## Local check Package built by @@ -26,7 +32,7 @@ build() R CMD CHECK /Users/buurensv/Package/mice/mice_3.9.0.tar.gz ``` -This fails!? (although interactive building in Rstudio works fine) +Fails, although interactive building in Rstudio works fine ``` * installing *source* package ‘mice’ ... @@ -51,31 +57,104 @@ ERROR: lazy loading failed for package ‘mice’ * removing ‘/Users/buurensv/Dropbox/Package/mice/mice/mice.Rcheck/mice’ ``` -I do not understand this message. After upgrading the `R 4.0.0`, I refreshed all packages, as required. Re-installing `Rcpp` manually did not solve the problem. +I do not understand this message. After upgrading the `R 4.0.0`, I refreshed all packages, as required. Re-installing `Rcpp` manually did not solve the problem. I will assume it is a false positive. -## Test environments - -* local OS X install, 10.15.4, R 4.0.0 -* win-builder, using `devtools::check_win_devel()` -Status: +## win-builder +```r +devtools::check_win_devel() ``` -``` +Status: OK + +## Rhub checks ```{r eval=FALSE} check_rhub() ``` -The upload failed. +``` +mice 3.9.0: NOTE +Build ID: mice_3.9.0.tar.gz-96a5a0f7e247483493124db3ee412d47 +Platform: Windows Server 2008 R2 SP1, R-devel, 32/64 bit + +* checking examples ... +** running examples for arch 'i386' ... NOTE +Examples with CPU (user + system) or elapsed time > 5s +D1 5.58 0.05 5.68 + user system elapsed +** running examples for arch 'x64' ... NOTE +Examples with CPU (user + system) or elapsed time > 5s + user system elapsed +D1 5.7 0.06 5.77 +``` + +``` +mice 3.9.0: NOTE +Build ID: mice_3.9.0.tar.gz-76d8ae5abbb941fc816b6716061457f4 +Platform: Ubuntu Linux 16.04 LTS, R-release, GCC + +* checking examples ... NOTE +Examples with CPU or elapsed time > 5s + user system elapsed +D1 3.908 0.136 7.817 +D3 3.036 0.044 6.117 +D2 3.000 0.020 5.797 +** found \donttest examples: check also with --run-donttest +``` ``` -─ Uploading package -Error in query("SUBMIT PACKAGE", data = list(email = unbox(email), token = unbox(email_get_token(email)), : - Email address not validated +mice 3.9.0: ERROR +Build ID: mice_3.9.0.tar.gz-91b0be74f9784bf484650eebf312a8b8 +Platform: Fedora Linux, R-devel, clang, gfortran + +* checking examples ... ERROR +Running examples in ‘mice-Ex.R’ failed +The error most likely occurred in: + +> base::assign(".ptime", proc.time(), pos = "CheckExEnv") +> ### Name: mice.impute.2l.bin +> ### Title: Imputation by a two-level logistic model using 'glmer' +> ### Aliases: mice.impute.2l.bin +> ### Keywords: datagen > +> ### ** Examples +> +> library(tidyr) +> library(dplyr) + +Attaching package: ‘dplyr’ + +The following objects are masked from ‘package:stats’: + + filter, lag + +The following objects are masked from ‘package:base’: + + intersect, setdiff, setequal, union + +> data("toenail2") +> data <- tidyr::complete(toenail2, patientID, visit) %>% ++ tidyr::fill(treatment) %>% ++ dplyr::select(-time) %>% ++ dplyr::mutate(patientID = as.integer(patientID)) +Error in bquote(on.exit({ : 'where' must be an environment +Calls: %>% ... replace_na -> -> eval_bare -> exit_handler -> bquote +Execution halted +``` + +This error is in `dplyr` code execution. I don't think I can solve it. + +``` +mice 3.9.0: PREPERROR +Build ID: mice_3.9.0.tar.gz-9aa8a9462c524b0dad4e60c9f2684fed +Platform: Debian Linux, R-devel, GCC ASAN/UBSAN + +Status for build mice_3.9.0.tar.gz-9aa8a9462c524b0dad4e60c9f2684fed +Status: success +Duration: 1 hour 34 minutes 26.3 seconds ``` ## Downstream dependencies @@ -158,4 +237,4 @@ revdep_summary() |MissingDataGUI |0.2-5 |1 | | | |Replication |0.1.2 |1 | | | -See +These package require additional software to be installed. See for details. diff --git a/cran-comments.md b/cran-comments.md index 76b06aca7..ba5700bd7 100644 --- a/cran-comments.md +++ b/cran-comments.md @@ -1,234 +1,20 @@ cran-comments ================ -## This is resubmission 2 +## `mice 3.9.0`, new submission -This is resubmitted after the resubmission 1 was cancelled due to a -miscommunication. - -There are two remaining problems (problems 2 (`hot.deck`) and 3 -(`miceadds`) below). I have contacted the package maintainers two weeks -ago, and both promised me to update. There is indeed a new version of -`miceadds` on CRAN, which supposedly solves the problem. I believe that -there should also be an update of `hot.deck`, though I haven’t yet seen -it on CRAN so that one is probably also in submission (I cant’t see -that). - -Hope this helps to get thing going again. - -## This is resubmission 1 - -### Problem 1 - - Changes to worse in reverse depends: - - Package: HardyWeinberg - Check: re-building of vignette outputs - New result: WARNING - Error(s) in re-building vignettes: - ... - --- re-building ‘HardyWeinberg.Rnw’ using Sweave - Loading required package: mice - - Attaching package: 'mice' - - The following objects are masked from 'package:base': - - cbind, rbind - - Loading required package: Rsolnp - Installing package into '/home/hornik/tmp/scratch/Rtmp2Owdzw/RLIBS_49de7c0e46e9' - (as 'lib' is unspecified) - - Error: processing vignette 'HardyWeinberg.Rnw' failed with diagnostics: - chunk 14 - Error in contrib.url(repos, type) : - trying to use CRAN without setting a mirror - - --- failed re-building 'HardyWeinberg.Rnw' - - SUMMARY: processing the following file failed: - 'HardyWeinberg.Rnw' - - Error: Vignette re-building failed. - Execution halted - - Package: MatchIt.mice - Check: examples - New result: ERROR - Running examples in ‘MatchIt.mice-Ex.R’ failed - The error most likely occurred in: - - base::assign(".ptime", proc.time(), pos = "CheckExEnv") - ### Name: matchitmice - ### Title: Matches Multiply Imputed Datasets - ### Aliases: matchitmice - ### Keywords: function - - ### ** Examples - - #Loading the 'dt.osa' dataset - data(dt.osa) - - #Imputing missing data points in the'dt.osa' dataset - datasets <- mice(dt.osa, m = 5, maxit = 1, - + method = c("", "", "mean", "", "polyreg", "logreg", "logreg")) - - iter imp variable - 1 1 BMI RAC - Installing 'nnet' package... - Installing package into ‘/home/hornik/tmp/scratch/Rtmpfgdy3y/RLIBS_4a054125c9bb’ - (as ‘lib’ is unspecified) - Error in contrib.url(repos, type) : - trying to use CRAN without setting a mirror - Calls: mice ... install.on.demand -> install.packages -> startsWith -> contrib.url - Execution halted - - Package: mipred - Check: tests - New result: ERROR - Running ‘testthat.R’ [3s/3s] - Running the tests in ‘tests/testthat.R’ failed. - Complete output: - library(testthat) - library(mipred) - - test_check("mipred") - NULL - - Installing 'nnet' package... - ── 1. Error: argument m in mice.options is ignored (@test-inputchecking-mipred.R - trying to use CRAN without setting a mirror - Backtrace: - 1. testthat::expect_warning(...) - 6. mipred::mipred(...) - 7. mipred:::.glm.mipred.cmb1(...) - 8. mipred:::.impute(...) - 9. mice::mice(...) - 10. mice:::sampler(...) - 11. mice:::sampler.univ(...) - 13. mice::mice.impute.polyreg(...) - 14. mice:::install.on.demand("nnet", ...) - 15. utils::install.packages(pkg, quiet = quiet) - 17. utils::contrib.url(repos, type) - - NULL - - Installing 'nnet' package... - ── 2. Error: argument m in mice.options is ignored (@test-inputchecking-mipred.c - trying to use CRAN without setting a mirror - Backtrace: - 1. testthat::expect_warning(...) - 6. mipred::mipred.cv(...) - 7. mipred:::.glm.mipred.cmb1.cv(...) - 8. mipred:::.impute(...) - 9. mice::mice(...) - 10. mice:::sampler(...) - 11. mice:::sampler.univ(...) - 13. mice::mice.impute.polyreg(...) - 14. mice:::install.on.demand("nnet", ...) - 15. utils::install.packages(pkg, quiet = quiet) - 17. utils::contrib.url(repos, type) - - ══ testthat results ════════════════ - -I fixed the `trying to use CRAN without setting a mirror` error in -`mice:::install.on.demand()` by including the `repos` argument. - -### Problem 2 - - Package: hot.deck - Check: re-building of vignette outputs - New result: WARNING - Error(s) in re-building vignettes: - ... - --- re-building ‘Using_Hot_Deck_Data.Rnw’ using Sweave - Loading required package: mice - - Attaching package: 'mice' - - The following objects are masked from 'package:base': - - cbind, rbind - - Warning in hot.deck(isq99, sdCutoff = 3, IDvars = c("IDORIGIN", "YEAR")) : - 52 observations with no observed data. These observations were removed - - Warning in hot.deck(isq99, sdCutoff = 3, IDvars = c("IDORIGIN", "YEAR")) : - 45 of 4661 imputations with # donors < 5, consider increasing sdCutoff or using method='p.draw' - - Loading required package: survival - * miceadds 3.7-6 (2019-12-15 13:38:43) - Warning: Number of logged events: 1 - - Error: processing vignette 'Using_Hot_Deck_Data.Rnw' failed with diagnostics: - chunk 10 (label = conv) - Error in Math.data.frame(structure(list(term = structure(1:12, .Label = c("(Intercept)", : - non-numeric variable(s) in data frame: term - - --- failed re-building 'Using_Hot_Deck_Data.Rnw' - - SUMMARY: processing the following file failed: - 'Using_Hot_Deck_Data.Rnw' - - Error: Vignette re-building failed. - Execution halted - -I found this error before, and am in contact with the package maintainer -for a solution (which is simple). - -### Problem 3 - - Package: miceadds - Check: examples - New result: ERROR - Running examples in ‘miceadds-Ex.R’ failed - The error most likely occurred in: - - base::assign(".ptime", proc.time(), pos = "CheckExEnv") - ### Name: jomo2datlist - ### Title: Converts a 'jomo' Data Frame in Long Format into a List of - ### Datasets or an Object of Class 'mids' - ### Aliases: jomo2datlist jomo2mids - - ### ** Examples - - ############################################################################# - # EXAMPLE 1: Dataset nhanes | jomo imputation and conversion into a data list - ############################################################################# - - data( nhanes, package="mice") - dat <- nhanes - - # impute under multivariate normal model in jomo - imp1 <- jomo::jomo1con(Y=dat, nburn=100, nbetween=10, nimp=5) - Error in loadNamespace(name) : there is no package called ‘jomo’ - Calls: :: ... loadNamespace -> withRestarts -> withOneRestart -> doWithOneRestart - Execution halted - -`mice 3.8.0` removes dependencies, and does not automatically install -anymore the `jomo` package. I have alerted the `miceadds` package -maintainer, and asked for a fix (which is simple). The maintainer -responded to have it fixed by next week. - -### Problem 4 - -`mice 3.7.0` gives an error in - - -This error is particular to `r-patches-solaris-x86`. I cannot reproduce -and have therefore put the example code in `dontrun`. - -### Problem 5 +## Reason -`testthat` produced four warnings. This is now fixed. +This update `mice 3.9.0` adds new functionality, reduces dependencies +and provides solutions for issues found in `mice 3.8.0` and before. -## Reason +## Test environments -This update `mice 3.8.0` adds new functionality, reduces dependencies -and provides solutions for issues found in `mice 3.7.0` and before. + - local OS X install, 10.15.4, R 4.0.0 + - win-builder + - Rhub -## Checks +## Local check Package built by @@ -238,67 +24,202 @@ build() ``` ``` bash -R CMD CHECK /Users/buurensv/Package/mice/mice_3.8.0.tar.gz +R CMD CHECK /Users/buurensv/Package/mice/mice_3.9.0.tar.gz ``` -Status: OK - -## Test environments +Fails, although interactive building in Rstudio works fine + + * installing *source* package ‘mice’ ... + ** using staged installation + ** libs + clang++ -mmacosx-version-min=10.13 -std=gnu++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I'/Users/buurensv/Library/R/3.6/library/Rcpp/include' -I/usr/local/include -fPIC -Wall -g -O2 -c RcppExports.cpp -o RcppExports.o + clang++ -mmacosx-version-min=10.13 -std=gnu++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I'/Users/buurensv/Library/R/3.6/library/Rcpp/include' -I/usr/local/include -fPIC -Wall -g -O2 -c match.cpp -o match.o + Error: package ‘Rcpp’ was installed before R 4.0.0: please re-install it + Execution halted + clang++ -mmacosx-version-min=10.13 -std=gnu++11 -dynamiclib -Wl,-headerpad_max_install_names -undefined dynamic_lookup -single_module -multiply_defined suppress -L/Library/Frameworks/R.framework/Resources/lib -L/usr/local/lib -o mice.so RcppExports.o match.o -F/Library/Frameworks/R.framework/.. -framework R -Wl,-framework -Wl,CoreFoundation + Error: package ‘Rcpp’ was installed before R 4.0.0: please re-install it + Execution halted + installing to /Users/buurensv/Dropbox/Package/mice/mice/mice.Rcheck/00LOCK-mice/00new/mice/libs + ** R + ** data + *** moving datasets to lazyload DB + ** inst + ** byte-compile and prepare package for lazy loading + Error: package ‘broom’ was installed before R 4.0.0: please re-install it + Execution halted + ERROR: lazy loading failed for package ‘mice’ + * removing ‘/Users/buurensv/Dropbox/Package/mice/mice/mice.Rcheck/mice’ + +I do not understand this message. After upgrading the `R 4.0.0`, I +refreshed all packages, as required. Re-installing `Rcpp` manually did +not solve the problem. I will assume it is a false positive. + +## win-builder - - local OS X install, 10.15.3, R 3.6.2 - - win-builder, using `devtools::check_win_devel()` +``` r +devtools::check_win_devel() +``` -Status: +Status: OK - Failed to upload/or report +## Rhub checks ``` r check_rhub() ``` -Status: Two “succes”, two “error”, but it’s not clear to me whether -these are related to `mice`. + mice 3.9.0: NOTE + Build ID: mice_3.9.0.tar.gz-96a5a0f7e247483493124db3ee412d47 + Platform: Windows Server 2008 R2 SP1, R-devel, 32/64 bit + + * checking examples ... + ** running examples for arch 'i386' ... NOTE + Examples with CPU (user + system) or elapsed time > 5s + D1 5.58 0.05 5.68 + user system elapsed + ** running examples for arch 'x64' ... NOTE + Examples with CPU (user + system) or elapsed time > 5s + user system elapsed + D1 5.7 0.06 5.77 + + mice 3.9.0: NOTE + Build ID: mice_3.9.0.tar.gz-76d8ae5abbb941fc816b6716061457f4 + Platform: Ubuntu Linux 16.04 LTS, R-release, GCC + + * checking examples ... NOTE + Examples with CPU or elapsed time > 5s + user system elapsed + D1 3.908 0.136 7.817 + D3 3.036 0.044 6.117 + D2 3.000 0.020 5.797 + ** found \donttest examples: check also with --run-donttest + + mice 3.9.0: ERROR + Build ID: mice_3.9.0.tar.gz-91b0be74f9784bf484650eebf312a8b8 + Platform: Fedora Linux, R-devel, clang, gfortran + + * checking examples ... ERROR + Running examples in ‘mice-Ex.R’ failed + The error most likely occurred in: + + > base::assign(".ptime", proc.time(), pos = "CheckExEnv") + > ### Name: mice.impute.2l.bin + > ### Title: Imputation by a two-level logistic model using 'glmer' + > ### Aliases: mice.impute.2l.bin + > ### Keywords: datagen + > + > ### ** Examples + > + > library(tidyr) + > library(dplyr) + + Attaching package: ‘dplyr’ + + The following objects are masked from ‘package:stats’: + + filter, lag + + The following objects are masked from ‘package:base’: + + intersect, setdiff, setequal, union + + > data("toenail2") + > data <- tidyr::complete(toenail2, patientID, visit) %>% + + tidyr::fill(treatment) %>% + + dplyr::select(-time) %>% + + dplyr::mutate(patientID = as.integer(patientID)) + Error in bquote(on.exit({ : 'where' must be an environment + Calls: %>% ... replace_na -> -> eval_bare -> exit_handler -> bquote + Execution halted + +This error is in `dplyr` code execution. I don’t think I can solve it. + + mice 3.9.0: PREPERROR + Build ID: mice_3.9.0.tar.gz-9aa8a9462c524b0dad4e60c9f2684fed + Platform: Debian Linux, R-devel, GCC ASAN/UBSAN + + Status for build mice_3.9.0.tar.gz-9aa8a9462c524b0dad4e60c9f2684fed + Status: success + Duration: 1 hour 34 minutes 26.3 seconds ## Downstream dependencies I have run ``` r -library("revdepcheck") -revdepcheck::revdep_reset() +library(revdepcheck) +revdep_reset() revdep_check(num_workers = 3) revdep_summary() ``` -There were 63 reverse dependencies. - -## Failed to check (2) +### `problems.md` + + *Wow, no problems at all. :)* + +### README.md + +# Platform + +| field | value | +| :------- | :--------------------------- | +| version | R version 4.0.0 (2020-04-24) | +| os | macOS Catalina 10.15.4 | +| system | x86\_64, darwin17.0 | +| ui | RStudio | +| language | (EN) | +| collate | en\_US.UTF-8 | +| ctype | en\_US.UTF-8 | +| tz | Europe/Amsterdam | +| date | 2020-05-14 | + +# Dependencies + +| package | old | new | Δ | +| :--------- | :------- | :------- | :- | +| mice | 3.8.0 | 3.9.0 | \* | +| assertthat | 0.2.1 | 0.2.1 | | +| backports | 1.1.7 | 1.1.7 | | +| BH | 1.72.0-3 | 1.72.0-3 | | +| broom | 0.5.6 | 0.5.6 | | +| cli | 2.0.2 | 2.0.2 | | +| crayon | 1.3.4 | 1.3.4 | | +| digest | 0.6.25 | 0.6.25 | | +| dplyr | 0.8.5 | 0.8.5 | | +| ellipsis | 0.3.0 | 0.3.0 | | +| fansi | 0.4.1 | 0.4.1 | | +| generics | 0.0.2 | 0.0.2 | | +| glue | 1.4.1 | 1.4.1 | | +| lifecycle | 0.2.0 | 0.2.0 | | +| magrittr | 1.5 | 1.5 | | +| pillar | 1.4.4 | 1.4.4 | | +| pkgconfig | 2.0.3 | 2.0.3 | | +| plogr | 0.2.0 | 0.2.0 | | +| plyr | 1.8.6 | 1.8.6 | | +| purrr | 0.3.4 | 0.3.4 | | +| R6 | 2.4.1 | 2.4.1 | | +| Rcpp | 1.0.4.6 | 1.0.4.6 | | +| reshape2 | 1.4.4 | 1.4.4 | | +| rlang | 0.4.6 | 0.4.6 | | +| stringi | 1.4.6 | 1.4.6 | | +| stringr | 1.4.0 | 1.4.0 | | +| tibble | 3.0.1 | 3.0.1 | | +| tidyr | 1.0.3 | 1.0.3 | | +| tidyselect | 1.1.0 | 1.1.0 | | +| utf8 | 1.1.4 | 1.1.4 | | +| vctrs | 0.3.0 | 0.3.0 | | + +## Revdeps + +### Failed to check (4) | package | version | error | warning | note | | :------------- | :-------- | :---- | :------ | :--- | +| brms | 2.12.0 | 1 | | 1 | | dynr | 0.1.15-25 | 1 | | | | MissingDataGUI | 0.2-5 | 1 | | | +| Replication | 0.1.2 | 1 | | | -The reason is that these package do not install locally on my -system. - -## New problems (3) - -| package | version | error | warning | note | -| :--------------------------------------------- | :------ | :----- | :------ | :--- | -| [CALIBERrfimpute](problems.md#caliberrfimpute) | 1.0-1 | **+1** | | | -| [cobalt](problems.md#cobalt) | 4.0.0 | **+1** | | | -| [hot.deck](problems.md#hotdeck) | 1.1 | **+1** | | | - -`CALIBERrfimpute` is archived on CRAN. - -The `cobalt` problem is caused by a change in `mice::complete()`. There -is a new name clash between the `MatchThem` and `mice 3.8.0`, and -`cobalt` uses both packages. I have noted the `MatchThem` maintainer, -and suggested a fix. The maintainer responded that he would look into -it. - -The `hot.deck` problem is caused by a change in the -`mice::summary.mira()` function. I have noted the `hot.deck` maintainer, -and suggested a fix. The maintainer said he’d submitted an update to -CRAN. +These package require additional software to be installed. See + +for details.