diff --git a/cran-comments.Rmd b/cran-comments.Rmd
index 5dde87992..3df9f65a5 100644
--- a/cran-comments.Rmd
+++ b/cran-comments.Rmd
@@ -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
@@ -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
@@ -59,15 +72,15 @@ 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)
@@ -75,47 +88,295 @@ 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
+
+
+
+* 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
+
+
+
+## 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
+
+
+
+* 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
+
+
+
+## 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
+
+
+
+* 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
+
+
+
+## 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
-* 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
## 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
+
+
+
+* 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
+
+
+
+## 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.
+
diff --git a/cran-comments.md b/cran-comments.md
index 3be797c9a..c9374c4e4 100644
--- a/cran-comments.md
+++ b/cran-comments.md
@@ -1,22 +1,67 @@
cran-comments
================
-## mice 3.14.0
+## mice 3.15.0
New submission.
## Reason
-A report from CRAN indicates that `install.on.demand()` breaks the CRAN
-work flow, so an urgent update is needed. In addition, there are many
-changes and improvements since the last CRAN version 3.13.0 published in
-Jan 2021.
+`mice 3.15.0` contains many changes and enhancements over `mice 3.14.0`
## Test environments
-- local OS X install, 11.6, R 4.1.2
-- win-builder
-- Rhub
+### Local
+
+``` r
+R.Version()
+```
+
+ ## $platform
+ ## [1] "aarch64-apple-darwin20"
+ ##
+ ## $arch
+ ## [1] "aarch64"
+ ##
+ ## $os
+ ## [1] "darwin20"
+ ##
+ ## $system
+ ## [1] "aarch64, darwin20"
+ ##
+ ## $status
+ ## [1] ""
+ ##
+ ## $major
+ ## [1] "4"
+ ##
+ ## $minor
+ ## [1] "2.2"
+ ##
+ ## $year
+ ## [1] "2022"
+ ##
+ ## $month
+ ## [1] "10"
+ ##
+ ## $day
+ ## [1] "31"
+ ##
+ ## $`svn rev`
+ ## [1] "83211"
+ ##
+ ## $language
+ ## [1] "R"
+ ##
+ ## $version.string
+ ## [1] "R version 4.2.2 (2022-10-31)"
+ ##
+ ## $nickname
+ ## [1] "Innocent and Trusting"
+
+### win-builder
+
+### \* Rhub
## Local check
@@ -28,7 +73,7 @@ build()
```
``` bash
-R CMD CHECK mice_3.14.0.tar.gz
+R CMD CHECK mice_3.15.0.tar.gz
```
Status: OK
@@ -39,7 +84,19 @@ Status: OK
devtools::check_win_devel()
```
-Status: OK
+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
@@ -49,13 +106,16 @@ devtools::check_rhub()
Results:
-1. Debian Linux, R-devel, GCC ASAN/UBSAN: Success
-2. Ubuntu Linux 20.04.1 LTS, R-release, GCC: Success
-3. Fedora Linux, R-devel, clang, gfortran: Success
+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
library(revdepcheck)
@@ -63,47 +123,291 @@ 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
-### `problems.md`
+
+
+ * 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
+
+
+
+ ## 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
+
+
+
+ * 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
+
+
+
+ ## In both
- # CALIBERrfimpute
+ * 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
- * Version: 1.0-5
+ * Version: 0.1.2
* GitHub: NA
- * Source code: https://github.com/cran/CALIBERrfimpute
- * Date/Publication: 2021-05-05 09:00:04
- * Number of recursive dependencies: 53
+ * 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
+
+
+
+ ## 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
- Run `revdep_details(, "CALIBERrfimpute")` for more info
+
+
+ * 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
## 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
+
+
+
+ * 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
+
+
+
+ ## 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
- \vspace{1em}
+ *** caught segfault ***
+ address 0x6c6c65432f6c6163, cause 'invalid permissions'
- When sourcing ‘simstudy_survival.R’:
- Error: missing value where TRUE/FALSE needed
- Execution halted
-
-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.
+ 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.