cran-comments.Rmd

---
title: "cran-comments"
output: github_document
---

```{r setup, include=FALSE}
knitr::opts_chunk$set(echo = TRUE)
```

## mice 3.15.0

New submission. 

## Reason

`mice 3.15.0` contains many changes and enhancements over `mice 3.14.0`

## Test environments

### Local

```{r}
R.Version()
```

### win-builder

### * Rhub

## Local check

Package built by

```{r eval = FALSE}
library("devtools")
build()
```

```{bash eval=FALSE}
R CMD CHECK mice_3.15.0.tar.gz
```

Status: OK

## win-builder

```{r eval=FALSE}
devtools::check_win_devel()
```

Status: 1 NOTE

```
Found the following (possibly) invalid URLs:
  URL: https://journals.sagepub.com/doi/10.1177/0049124118799376
    From: man/ampute.Rd
    Status: 503
    Message: Service Unavailable
  URL: https://journals.sagepub.com/doi/full/10.1177/0049124118799376
    From: man/ampute.Rd
    Status: 503
    Message: Service Unavailable
```

SvB: The URLs exist. I believe the NOTE is caused by blocking by SAGE.

## Rhub checks

```{r eval=FALSE}
devtools::check_rhub()
```

Results:

1. Debian Linux, R-devel, GCC ASAN/UBSAN: Build timed out (after 20 minutes). Marking the build as failed.
2. Windows Server 2022, R-devel, 64 bit: 0 errors ✔ | 0 warnings ✔ | 0 notes ✔
3. Ubuntu Linux 20.04.1 LTS, R-release, GCC: SUCCESS
4. Fedora Linux, R-devel, clang, gfortran: SUCCES


## Downstream dependencies

`mice` has 110 downstream dependencies

```{r eval=FALSE}
library(revdepcheck)
revdep_reset()
revdep_check(num_workers = 10)
```

```
OK: 108                                                                                                                                                    
BROKEN: 2
Total time: 22 min
── REPORT ───────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────
Writing summary to 'revdep/README.md'
Writing problems to 'revdep/problems.md'
Writing failures to 'revdep/failures.md'
Writing CRAN report to 'revdep/cran.md'
```

### `failures.md`

```
# dynr

<details>

* Version: 0.1.16-91
* GitHub: https://github.com/mhunter1/dynr
* Source code: https://github.com/cran/dynr
* Date/Publication: 2022-10-17 07:02:35 UTC
* Number of recursive dependencies: 120

Run `revdepcheck::revdep_details(, "dynr")` for more info

</details>

## In both

*   checking whether package ‘dynr’ can be installed ... ERROR

    Installation failed.
    See ‘/Users/buurensv/Dropbox/Package/mice/mice/revdep/checks.noindex/dynr/new/dynr.Rcheck/00install.out’ for details.

## Installation

### Devel

* installing *source* package ‘dynr’ ...
** package ‘dynr’ successfully unpacked and MD5 sums checked
** using staged installation
checking for gsl-config... no
configure: error: gsl-config not found, is GSL installed?
ERROR: configuration failed for package ‘dynr’
* removing ‘/Users/buurensv/Dropbox/Package/mice/mice/revdep/checks.noindex/dynr/new/dynr.Rcheck/dynr’


### CRAN

* installing *source* package ‘dynr’ ...
** package ‘dynr’ successfully unpacked and MD5 sums checked
** using staged installation
checking for gsl-config... no
configure: error: gsl-config not found, is GSL installed?
ERROR: configuration failed for package ‘dynr’
* removing ‘/Users/buurensv/Dropbox/Package/mice/mice/revdep/checks.noindex/dynr/old/dynr.Rcheck/dynr’


# pguIMP

<details>

* Version: 0.0.0.3
* GitHub: https://github.com/SMLMS/pguIMP
* Source code: https://github.com/cran/pguIMP
* Date/Publication: 2021-09-30 11:50:02 UTC
* Number of recursive dependencies: 221

Run `revdepcheck::revdep_details(, "pguIMP")` for more info

</details>

## In both

*   checking whether package ‘pguIMP’ can be installed ... ERROR

    Installation failed.
    See ‘/Users/buurensv/Dropbox/Package/mice/mice/revdep/checks.noindex/pguIMP/new/pguIMP.Rcheck/00install.out’ for details.

## Installation

### Devel

* installing *source* package ‘pguIMP’ ...
** package ‘pguIMP’ successfully unpacked and MD5 sums checked
** using staged installation
** R
** inst
** byte-compile and prepare package for lazy loading
Error: .onLoad failed in loadNamespace() for 'rJava', details:
  call: dyn.load(jli, FALSE)
  error: unable to load shared object '/Library/Java/JavaVirtualMachines/jdk1.8.0_144.jdk/Contents/Home/jre/lib/jli/libjli.dylib':
  dlopen(/Library/Java/JavaVirtualMachines/jdk1.8.0_144.jdk/Contents/Home/jre/lib/jli/libjli.dylib, 0x000A): tried: '/Library/Java/JavaVirtualMachines/jdk1.8.0_144.jdk/Contents/Home/jre/lib/jli/libjli.dylib' (mach-o file, but is an incompatible architecture (have 'x86_64', need 'arm64')), '/System/Volumes/Preboot/Cryptexes/OS/Library/Java/JavaVirtualMachines/jdk1.8.0_144.jdk/Contents/Home/jre/lib/jli/libjli.dylib' (no such file), '/Library/Java/JavaVirtualMachines/jdk1.8.0_144.jdk/Contents/Home/jre/lib/jli/libjli.dylib' (mach-o file, but is an incompatible architecture (have 'x86_64', need 'arm64'))
Execution halted
ERROR: lazy loading failed for package ‘pguIMP’
* removing ‘/Users/buurensv/Dropbox/Package/mice/mice/revdep/checks.noindex/pguIMP/new/pguIMP.Rcheck/pguIMP’


### CRAN

* installing *source* package ‘pguIMP’ ...
** package ‘pguIMP’ successfully unpacked and MD5 sums checked
** using staged installation
** R
** inst
** byte-compile and prepare package for lazy loading
Error: .onLoad failed in loadNamespace() for 'rJava', details:
  call: dyn.load(jli, FALSE)
  error: unable to load shared object '/Library/Java/JavaVirtualMachines/jdk1.8.0_144.jdk/Contents/Home/jre/lib/jli/libjli.dylib':
  dlopen(/Library/Java/JavaVirtualMachines/jdk1.8.0_144.jdk/Contents/Home/jre/lib/jli/libjli.dylib, 0x000A): tried: '/Library/Java/JavaVirtualMachines/jdk1.8.0_144.jdk/Contents/Home/jre/lib/jli/libjli.dylib' (mach-o file, but is an incompatible architecture (have 'x86_64', need 'arm64')), '/System/Volumes/Preboot/Cryptexes/OS/Library/Java/JavaVirtualMachines/jdk1.8.0_144.jdk/Contents/Home/jre/lib/jli/libjli.dylib' (no such file), '/Library/Java/JavaVirtualMachines/jdk1.8.0_144.jdk/Contents/Home/jre/lib/jli/libjli.dylib' (mach-o file, but is an incompatible architecture (have 'x86_64', need 'arm64'))
Execution halted
ERROR: lazy loading failed for package ‘pguIMP’
* removing ‘/Users/buurensv/Dropbox/Package/mice/mice/revdep/checks.noindex/pguIMP/old/pguIMP.Rcheck/pguIMP’


# Replication

<details>

* Version: 0.1.2
* GitHub: NA
* Source code: https://github.com/cran/Replication
* Date/Publication: 2020-04-09 12:10:02 UTC
* Number of recursive dependencies: 90

Run `revdepcheck::revdep_details(, "Replication")` for more info

</details>

## In both

*   checking whether package ‘Replication’ can be installed ... ERROR
    Installation failed.
    See ‘/Users/buurensv/Dropbox/Package/mice/mice/revdep/checks.noindex/Replication/new/Replication.Rcheck/00install.out’ for details.

## Installation

### Devel

* installing *source* package ‘Replication’ ...
** package ‘Replication’ successfully unpacked and MD5 sums checked
** using staged installation
** R
** byte-compile and prepare package for lazy loading
Error: .onLoad failed in loadNamespace() for 'rjags', details:
  call: dyn.load(file, DLLpath = DLLpath, ...)
  error: unable to load shared object '/Users/buurensv/Dropbox/Package/mice/mice/revdep/library.noindex/Replication/rjags/libs/rjags.so':
  dlopen(/Users/buurensv/Dropbox/Package/mice/mice/revdep/library.noindex/Replication/rjags/libs/rjags.so, 0x000A): Library not loaded: /usr/local/lib/libjags.4.dylib
  Referenced from: <82D1D1F8-CC85-3273-A9BC-B86843329438> /Users/buurensv/Dropbox/Package/mice/mice/revdep/library.noindex/Replication/rjags/libs/rjags.so
  Reason: tried: '/usr/local/lib/libjags.4.dylib' (mach-o file, but is an incompatible architecture (have 'x86_64', need 'arm64')), '/System/Volumes/Preboot/Cryptexes/OS/usr/local/lib/libjags.4.dylib' (no such file), '/usr/local/lib/libjags.4.dylib' (mach-o file, but is an incompatible architecture (have 'x86_64', need 'arm64')), '/Library/Frameworks/R.framework/Resources/lib/libjags.4.dylib' (no such file), '/Library/Java/Jav
Execution halted
ERROR: lazy loading failed for package ‘Replication’
* removing ‘/Users/buurensv/Dropbox/Package/mice/mice/revdep/checks.noindex/Replication/new/Replication.Rcheck/Replication’


### CRAN

* installing *source* package ‘Replication’ ...
** package ‘Replication’ successfully unpacked and MD5 sums checked
** using staged installation
** R
** byte-compile and prepare package for lazy loading
Error: .onLoad failed in loadNamespace() for 'rjags', details:
  call: dyn.load(file, DLLpath = DLLpath, ...)
  error: unable to load shared object '/Users/buurensv/Dropbox/Package/mice/mice/revdep/library.noindex/Replication/rjags/libs/rjags.so':
  dlopen(/Users/buurensv/Dropbox/Package/mice/mice/revdep/library.noindex/Replication/rjags/libs/rjags.so, 0x000A): Library not loaded: /usr/local/lib/libjags.4.dylib
  Referenced from: <82D1D1F8-CC85-3273-A9BC-B86843329438> /Users/buurensv/Dropbox/Package/mice/mice/revdep/library.noindex/Replication/rjags/libs/rjags.so
  Reason: tried: '/usr/local/lib/libjags.4.dylib' (mach-o file, but is an incompatible architecture (have 'x86_64', need 'arm64')), '/System/Volumes/Preboot/Cryptexes/OS/usr/local/lib/libjags.4.dylib' (no such file), '/usr/local/lib/libjags.4.dylib' (mach-o file, but is an incompatible architecture (have 'x86_64', need 'arm64')), '/Library/Frameworks/R.framework/Resources/lib/libjags.4.dylib' (no such file), '/Library/Java/Jav
Execution halted
ERROR: lazy loading failed for package ‘Replication’
* removing ‘/Users/buurensv/Dropbox/Package/mice/mice/revdep/checks.noindex/Replication/old/Replication.Rcheck/Replication’
```

SvB: I believe that none of these issues are attributable to `mice`.


### `problems.md`

```
# adjustedCurves

<details>

* Version: 0.9.0
* GitHub: https://github.com/RobinDenz1/adjustedCurves
* Source code: https://github.com/cran/adjustedCurves
* Date/Publication: 2022-09-22 08:40:13 UTC
* Number of recursive dependencies: 167

Run `revdepcheck::revdep_details(, "adjustedCurves")` for more info

</details>

## Newly broken

*   checking tests ...
      Running ‘testthat.R’
     ERROR
    Running the tests in ‘tests/testthat.R’ failed.
    Last 13 lines of output:
        5. ├─dplyr:::summarise.grouped_df(...)
        6. │ └─dplyr:::summarise_cols(.data, dplyr_quosures(...), caller_env = caller_env())
        7. │   ├─base::withCallingHandlers(...)
        8. │   └─dplyr:::map(quosures, summarise_eval_one, mask = mask)
        9. │     └─base::lapply(.x, .f, ...)
       10. │       └─dplyr (local) FUN(X[[i]], ...)
       11. │         └─mask$eval_all_summarise(quo)
       12. ├─adjustedCurves:::pool_p_values(p_val)
       13. └─base::.handleSimpleError(...)
       14.   └─dplyr (local) h(simpleError(msg, call))
       15.     └─rlang::abort(bullets, call = error_call, parent = skip_internal_condition(e))
      
      [ FAIL 7 | WARN 126 | SKIP 125 | PASS 1579 ]
      Error: Test failures
      Execution halted

# bipd

<details>

* Version: 0.3
* GitHub: NA
* Source code: https://github.com/cran/bipd
* Date/Publication: 2022-06-05 16:10:05 UTC
* Number of recursive dependencies: 107

Run `revdepcheck::revdep_details(, "bipd")` for more info

</details>

## Newly broken

*   checking dependencies in R code ...sh: line 1: 26776 Segmentation fault: 11  R_DEFAULT_PACKAGES=NULL '/Library/Frameworks/R.framework/Resources/bin/R' --vanilla --no-echo 2>&1 < '/var/folders/5_/g85d42yj50b6lrjq4rzjzg8w0000gn/T//RtmpKRyE8b/file66d821b07fdc'
     NOTE
    
     *** caught segfault ***
    address 0x6c6c65432f6c6163, 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)
    ...
     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 ...

## Newly fixed

*   checking dependencies in R code ...sh: line 1: 26657 Segmentation fault: 11  R_DEFAULT_PACKAGES=NULL '/Library/Frameworks/R.framework/Resources/bin/R' --vanilla --no-echo 2>&1 < '/var/folders/5_/g85d42yj50b6lrjq4rzjzg8w0000gn/T//Rtmpi8gCya/file6689272a04f8'
     NOTE
    
     *** caught segfault ***
    address 0x6c6c65432f6c6163, 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)
    ...
     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 ...
```

#### Action taken

##### adjustedCurves

SvB: I contacted the maintainer on 14/11 and he explained that the error is due to hard-coded values in some of the tests in `adjustedCurves`. Since the random generator has changed in `mice 3.15.0`, these tests now fail. I interpret the error as expected behaviour.

#####  bipd

SvB: This problem seems to be a configuration or memory issue, not related to `mice`. I took no further action.