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Update cran-comments to mice 3.15.0
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@stefvanbuuren
stefvanbuuren committed Nov 17, 2022
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Expand Up @@ -37,7 +37,7 @@ build()
```

```{bash eval=FALSE}
R CMD CHECK mice_3.14.15.tar.gz
R CMD CHECK mice_3.15.0.tar.gz
```

Status: OK
Expand All @@ -50,6 +50,19 @@ 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

Expand All @@ -59,63 +72,311 @@ devtools::check_rhub()

Results:

1. Debian Linux, R-devel, GCC ASAN/UBSAN:
2. Windows Server 2022, R-devel, 64 bit: **Success**
3. Ubuntu Linux 20.04.1 LTS, R-release, GCC:
4. Fedora Linux, R-devel, clang, gfortran:
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

I have run
`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`

There is one old failure (`dynr`): `configure: error: gsl-config not found, is GSL installed?`
Not related to `mice`.
```
# 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`

```
# CALIBERrfimpute
# adjustedCurves
<details>
* Version: 1.0-5
* GitHub: NA
* Source code: https://github.com/cran/CALIBERrfimpute
* Date/Publication: 2021-05-05 09:00:04
* Number of recursive dependencies: 53
* 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 `revdep_details(, "CALIBERrfimpute")` for more info
Run `revdepcheck::revdep_details(, "adjustedCurves")` for more info
</details>
## Newly broken
* checking running R code from vignettes ...
‘simstudy_survival.Rnw’ using ‘UTF-8’... failed
* checking tests ...
Running ‘testthat.R’
ERROR
Errors in running code in vignettes:
when running code in ‘simstudy_survival.Rnw’
...
x2 & 0.0391 & 0.0254 & 0.0138 \\
x3 & -0.0314 & -0.00854 & -0.0228 \\
\hline
\end{tabular}
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'
\vspace{1em}
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
When sourcing ‘simstudy_survival.R’:
Error: missing value where TRUE/FALSE needed
Execution halted
*** 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 ...
```

Not sure whether it's related to `mice`, and seems relatively benign if it is. The package maintainer of `CALIBERrfimpute` is aware of the problem, and will look into the issue.
#### 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.

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