Closed gH2AX closed 1 year ago
It seems reprex has its own issues..
> reprex(md.pattern(iris.mis))
ℹ Rendering reprex...
Error in `reprex_render()`:
! This reprex appears to crash R. Call `reprex()` again with `std_out_err = TRUE` to get more info.
Run `rlang::last_error()` to see where the error occurred.
> reprex(md.pattern(iris.mis), std_out_err = TRUE)
ℹ Rendering reprex...
sh: +RTS: command not found
Error: pandoc document conversion failed with error 127
In addition: Warning message:
In system(command) : error in running command
Can you provide some more info on the incomplete data? Perhaps share the data that reproduces the behaviour.
It's unspecific, I tried various datasets. But here's one expample:
The iris dataset is a built-in dataset in R. I have the version 4.2.2. I run the following commands:
library(missForest)
library(mice)
iris.mis = prodNA(iris, noNA = 0.1)
iris.mis = subset(iris.mis, select=-c(Species))
md.pattern(iris.mis)
caught segfault
I already re-installed the mice package from tar.gz - makes no difference. Everything else runs very smoothly..
Curious. I get various 'sprintf' is deprecated:
messages when building the package, but the code works on my machine. Perhaps you upgraded to Ventura and need to re-install tools?
library(missForest)
library(mice)
#>
#> Attaching package: 'mice'
#> The following object is masked from 'package:stats':
#>
#> filter
#> The following objects are masked from 'package:base':
#>
#> cbind, rbind
iris.mis = prodNA(iris, noNA = 0.1)
iris.mis = subset(iris.mis, select=-c(Species))
md.pattern(iris.mis)
#> Sepal.Width Sepal.Length Petal.Length Petal.Width
#> 95 1 1 1 1 0
#> 15 1 1 1 0 1
#> 10 1 1 0 1 1
#> 2 1 1 0 0 2
#> 12 1 0 1 1 1
#> 1 1 0 1 0 2
#> 1 1 0 0 1 2
#> 9 0 1 1 1 1
#> 1 0 1 1 0 2
#> 3 0 1 0 1 2
#> 1 0 0 1 1 2
#> 14 15 16 19 64
sessionInfo()
#> R version 4.2.1 (2022-06-23)
#> Platform: aarch64-apple-darwin20 (64-bit)
#> Running under: macOS Monterey 12.6
#>
#> Matrix products: default
#> BLAS: /Library/Frameworks/R.framework/Versions/4.2-arm64/Resources/lib/libRblas.0.dylib
#> LAPACK: /Library/Frameworks/R.framework/Versions/4.2-arm64/Resources/lib/libRlapack.dylib
#>
#> locale:
#> [1] en_US.UTF-8/en_US.UTF-8/en_US.UTF-8/C/en_US.UTF-8/en_US.UTF-8
#>
#> attached base packages:
#> [1] stats graphics grDevices utils datasets methods base
#>
#> other attached packages:
#> [1] mice_3.14.8 missForest_1.5
#>
#> loaded via a namespace (and not attached):
#> [1] Rcpp_1.0.9 pillar_1.8.1 compiler_4.2.1
#> [4] highr_0.9 R.methodsS3_1.8.2 R.utils_2.12.1
#> [7] iterators_1.0.14 tools_4.2.1 rngtools_1.5.2
#> [10] digest_0.6.30 lattice_0.20-45 tibble_3.1.8
#> [13] evaluate_0.18 lifecycle_1.0.3 R.cache_0.16.0
#> [16] pkgconfig_2.0.3 rlang_1.0.6 doRNG_1.8.2
#> [19] reprex_2.0.2 foreach_1.5.2 DBI_1.1.3
#> [22] cli_3.4.1 rstudioapi_0.14 yaml_2.3.6
#> [25] parallel_4.2.1 xfun_0.34 fastmap_1.1.0
#> [28] dplyr_1.0.10 withr_2.5.0 styler_1.8.0
#> [31] stringr_1.4.1 knitr_1.40 generics_0.1.3
#> [34] vctrs_0.5.0 fs_1.5.2 grid_4.2.1
#> [37] tidyselect_1.2.0 glue_1.6.2 R6_2.5.1
#> [40] fansi_1.0.3 rmarkdown_2.17 tidyr_1.2.1
#> [43] purrr_0.3.5 magrittr_2.0.3 backports_1.4.1
#> [46] codetools_0.2-18 htmltools_0.5.3 itertools_0.1-3
#> [49] assertthat_0.2.1 randomForest_4.7-1.1 utf8_1.2.2
#> [52] stringi_1.7.8 broom_1.0.1 R.oo_1.25.0
Created on 2022-11-09 with reprex v2.0.2
Still on Monterey.. what's the issue with tools? And how would I re-install it? It's a base-package and cannot be removed.
Can also not reproduce:
library(missForest)
library(mice)
iris.mis = prodNA(iris, noNA = 0.1)
iris.mis = subset(iris.mis, select=-c(Species))
md.pattern(iris.mis, rotate.names = TRUE)
#> Sepal.Length Sepal.Width Petal.Length Petal.Width
#> 97 1 1 1 1 0
#> 10 1 1 1 0 1
#> 14 1 1 0 1 1
#> 2 1 1 0 0 2
#> 11 1 0 1 1 1
#> 4 1 0 1 0 2
#> 1 1 0 0 1 2
#> 10 0 1 1 1 1
#> 1 0 0 1 0 3
#> 11 17 17 17 62
sessionInfo()
#> R version 4.2.2 (2022-10-31)
#> Platform: aarch64-apple-darwin20 (64-bit)
#> Running under: macOS Monterey 12.6
#>
#> Matrix products: default
#> BLAS: /Library/Frameworks/R.framework/Versions/4.2-arm64/Resources/lib/libRblas.0.dylib
#> LAPACK: /Library/Frameworks/R.framework/Versions/4.2-arm64/Resources/lib/libRlapack.dylib
#>
#> locale:
#> [1] en_US.UTF-8/en_US.UTF-8/en_US.UTF-8/C/en_US.UTF-8/en_US.UTF-8
#>
#> attached base packages:
#> [1] stats graphics grDevices utils datasets methods base
#>
#> other attached packages:
#> [1] mice_3.14.0 missForest_1.5
#>
#> loaded via a namespace (and not attached):
#> [1] Rcpp_1.0.9 compiler_4.2.2 pillar_1.7.0
#> [4] highr_0.9 iterators_1.0.14 tools_4.2.2
#> [7] rngtools_1.5.2 digest_0.6.29 lattice_0.20-45
#> [10] tibble_3.1.7 evaluate_0.15 lifecycle_1.0.1
#> [13] pkgconfig_2.0.3 rlang_1.0.3 doRNG_1.8.2
#> [16] reprex_2.0.2 foreach_1.5.2 DBI_1.1.2
#> [19] cli_3.3.0 rstudioapi_0.13 yaml_2.3.5
#> [22] parallel_4.2.2 xfun_0.31 fastmap_1.1.0
#> [25] withr_2.5.0 stringr_1.4.0 dplyr_1.0.9
#> [28] knitr_1.39 generics_0.1.3 fs_1.5.2
#> [31] vctrs_0.4.1 grid_4.2.2 tidyselect_1.1.2
#> [34] glue_1.6.2 R6_2.5.1 fansi_1.0.3
#> [37] rmarkdown_2.14 tidyr_1.2.0 purrr_0.3.4
#> [40] magrittr_2.0.3 backports_1.4.1 codetools_0.2-18
#> [43] htmltools_0.5.2 ellipsis_0.3.2 itertools_0.1-3
#> [46] assertthat_0.2.1 randomForest_4.7-1.1 utf8_1.2.2
#> [49] stringi_1.7.6 broom_1.0.0 crayon_1.5.1
Created on 2022-11-09 with reprex v2.0.2
Since it seems to be isolated to your R instance, and not to aarch64-apple-darwin20 (64-bit)
in general; perhaps a fresh install of the latest R framework would suffice.
@gH2AX You are not by any chance running R through Anaconda?
In general, you need the proper compilers if you are installing from source (mice
has some C and C++ code). You can get these from CRAN. I remember struggling a bit when switching to Apple's ARM CPU to get up and running.
@gH2AX You are not by any chance running R through Anaconda?
No, I am not running Anaconda.
[…] you need the proper compilers if you are installing from source […]
I only tried to compile from source once this error emerged..
I have a feeling that a clean install of the most recent R framework and RStudio would fix. Have you tried this?
The error you receive is not related to mice
, but stems from grDevices::dev.capabilities("semiTransparency")
.
Yes agree. What happens if you run
z <- grDevices::dev.capabilities("semiTransparency")
class(z)
#> [1] "list"
z
#> $semiTransparency
#> [1] TRUE
Created on 2022-11-11 with reprex v2.0.2
Yes agree. What happens if you run
z <- grDevices::dev.capabilities("semiTransparency") class(z) #> [1] "list" z #> $semiTransparency #> [1] TRUE
Created on 2022-11-11 with reprex v2.0.2
An empty (white) Quartz window opens. And I get the same output as you. Btw: If I call md.pattern() on a simple two-column numeric data.frame, it works! I will eventually try the clean install.
Hmm, interesting. I do not see a Quartz window.
I will close because we cannot reproduce and it's likely to be related to something outside mice
. Sorry, we cannot help, but thanks for bringing up the issue.
Feel free to reopen if you think it's mice-related.
Reinstalling xquartz
may help
I load a dataset in the variable 'ww', then when i call md.pattern(ww), my R session crashes with the following error message: