mpfr function in Rmpfr crashes R

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mpfr function in Rmpfr crashes R

Roger J. Bos
All,

The following code crashes by R on my mac with a message "R session
aborted.  A fatal error occured".

```
library(Rmpfr)
Rmpfr::mpfr(pi, 120)
```

Does anyone have any suggestions?   My session info is below:

R version 4.0.3 (2020-10-10)
Platform: x86_64-apple-darwin17.0 (64-bit)
Running under: macOS Big Sur 10.16

Matrix products: default
LAPACK:
/Library/Frameworks/R.framework/Versions/4.0/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] datasets  utils     stats     graphics  grDevices methods   base

other attached packages:
 [1] alphavantager_0.1.2 googlesheets4_0.2.0 googledrive_1.0.1
clipr_0.7.1
 [5] jsonlite_1.7.2      stringi_1.5.3       dtplyr_1.0.1
 data.table_1.13.6
 [9] dplyr_1.0.4         plyr_1.8.6          testthat_3.0.1
 lubridate_1.7.9.2
[13] timeDate_3043.102   sendmailR_1.2-1     rmarkdown_2.6
devtools_2.3.2
[17] usethis_2.0.0       xts_0.12.1          zoo_1.8-8
MASS_7.3-53
[21] fortunes_1.5-4

loaded via a namespace (and not attached):
 [1] tinytex_0.29      tidyselect_1.1.0  xfun_0.20         remotes_2.2.0
  purrr_0.3.4
 [6] gargle_0.5.0      lattice_0.20-41   generics_0.1.0    vctrs_0.3.6
  htmltools_0.5.1.1
[11] base64enc_0.1-3   rlang_0.4.10      pkgbuild_1.2.0    pillar_1.4.7
 glue_1.4.2
[16] withr_2.4.1       DBI_1.1.1         sessioninfo_1.1.1 lifecycle_0.2.0
  cellranger_1.1.0
[21] evaluate_0.14     memoise_2.0.0     knitr_1.31        callr_3.5.1
  fastmap_1.1.0
[26] ps_1.5.0          curl_4.3          Rcpp_1.0.6        openssl_1.4.3
  cachem_1.0.1
[31] desc_1.2.0        pkgload_1.1.0     fs_1.5.0          askpass_1.1
  digest_0.6.27
[36] processx_3.4.5    grid_4.0.3        rprojroot_2.0.2   cli_2.3.0
  tools_4.0.3
[41] magrittr_2.0.1    tibble_3.0.6      crayon_1.4.0      pkgconfig_2.0.3
  ellipsis_0.3.1
[46] prettyunits_1.1.1 httr_1.4.2        assertthat_0.2.1  R6_2.5.0
 compiler_4.0.3
19:05:52  >

Thanks,

Roger

        [[alternative HTML version deleted]]

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Re: mpfr function in Rmpfr crashes R

John Fox
Dear Roger,

This works perfectly fine for me on an apparently similar system, with
the exceptions that I'm running R 4.0.4, have many fewer packages
loaded, and am in a slightly different locale:

--------------- snip ------------

 > Rmpfr::mpfr(pi, 120)
1 'mpfr' number of precision  120   bits
[1] 3.1415926535897931159979634685441851616

 > sessionInfo()
R version 4.0.4 (2021-02-15)
Platform: x86_64-apple-darwin17.0 (64-bit)
Running under: macOS Big Sur 10.16

Matrix products: default
LAPACK:
/Library/Frameworks/R.framework/Versions/4.0/Resources/lib/libRlapack.dylib

locale:
[1] en_CA.UTF-8/en_CA.UTF-8/en_CA.UTF-8/C/en_CA.UTF-8/en_CA.UTF-8

attached base packages:
[1] stats     graphics  grDevices utils     datasets  methods   base

other attached packages:
[1] Rmpfr_0.8-2 gmp_0.6-2

loaded via a namespace (and not attached):
  [1] compiler_4.0.4    htmltools_0.5.1.1 tools_4.0.4       yaml_2.2.1
       rmarkdown_2.6
  [6] knitr_1.31        xfun_0.21         digest_0.6.27
packrat_0.5.0     rlang_0.4.10
[11] evaluate_0.14

--------------- snip ------------

You might try updating R or running Rmpfr in a cleaner session.

I hope this helps,
  John

John Fox, Professor Emeritus
McMaster University
Hamilton, Ontario, Canada
web: https://socialsciences.mcmaster.ca/jfox/

On 2021-03-06 7:07 p.m., Roger Bos wrote:

> All,
>
> The following code crashes by R on my mac with a message "R session
> aborted.  A fatal error occured".
>
> ```
> library(Rmpfr)
> Rmpfr::mpfr(pi, 120)
> ```
>
> Does anyone have any suggestions?   My session info is below:
>
> R version 4.0.3 (2020-10-10)
> Platform: x86_64-apple-darwin17.0 (64-bit)
> Running under: macOS Big Sur 10.16
>
> Matrix products: default
> LAPACK:
> /Library/Frameworks/R.framework/Versions/4.0/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] datasets  utils     stats     graphics  grDevices methods   base
>
> other attached packages:
>   [1] alphavantager_0.1.2 googlesheets4_0.2.0 googledrive_1.0.1
> clipr_0.7.1
>   [5] jsonlite_1.7.2      stringi_1.5.3       dtplyr_1.0.1
>   data.table_1.13.6
>   [9] dplyr_1.0.4         plyr_1.8.6          testthat_3.0.1
>   lubridate_1.7.9.2
> [13] timeDate_3043.102   sendmailR_1.2-1     rmarkdown_2.6
> devtools_2.3.2
> [17] usethis_2.0.0       xts_0.12.1          zoo_1.8-8
> MASS_7.3-53
> [21] fortunes_1.5-4
>
> loaded via a namespace (and not attached):
>   [1] tinytex_0.29      tidyselect_1.1.0  xfun_0.20         remotes_2.2.0
>    purrr_0.3.4
>   [6] gargle_0.5.0      lattice_0.20-41   generics_0.1.0    vctrs_0.3.6
>    htmltools_0.5.1.1
> [11] base64enc_0.1-3   rlang_0.4.10      pkgbuild_1.2.0    pillar_1.4.7
>   glue_1.4.2
> [16] withr_2.4.1       DBI_1.1.1         sessioninfo_1.1.1 lifecycle_0.2.0
>    cellranger_1.1.0
> [21] evaluate_0.14     memoise_2.0.0     knitr_1.31        callr_3.5.1
>    fastmap_1.1.0
> [26] ps_1.5.0          curl_4.3          Rcpp_1.0.6        openssl_1.4.3
>    cachem_1.0.1
> [31] desc_1.2.0        pkgload_1.1.0     fs_1.5.0          askpass_1.1
>    digest_0.6.27
> [36] processx_3.4.5    grid_4.0.3        rprojroot_2.0.2   cli_2.3.0
>    tools_4.0.3
> [41] magrittr_2.0.1    tibble_3.0.6      crayon_1.4.0      pkgconfig_2.0.3
>    ellipsis_0.3.1
> [46] prettyunits_1.1.1 httr_1.4.2        assertthat_0.2.1  R6_2.5.0
>   compiler_4.0.3
> 19:05:52  >
>
> Thanks,
>
> Roger
>
> [[alternative HTML version deleted]]
>
> ______________________________________________
> [hidden email] mailing list -- To UNSUBSCRIBE and more, see
> https://stat.ethz.ch/mailman/listinfo/r-help
> PLEASE do read the posting guide http://www.R-project.org/posting-guide.html
> and provide commented, minimal, self-contained, reproducible code.
>

______________________________________________
[hidden email] mailing list -- To UNSUBSCRIBE and more, see
https://stat.ethz.ch/mailman/listinfo/r-help
PLEASE do read the posting guide http://www.R-project.org/posting-guide.html
and provide commented, minimal, self-contained, reproducible code.
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Re: mpfr function in Rmpfr crashes R

Duncan Murdoch-2
In reply to this post by Roger J. Bos
It works for me, on a slightly different system than yours:

 > Rmpfr::mpfr(pi, 120)
1 'mpfr' number of precision  120   bits
[1] 3.1415926535897931159979634685441851616
 > sessionInfo()
R version 4.0.3 Patched (2021-01-30 r79912)
Platform: x86_64-apple-darwin17.0 (64-bit)
Running under: macOS Catalina 10.15.7

Matrix products: default
BLAS:
/Library/Frameworks/R.framework/Versions/4.0/Resources/lib/libRblas.dylib
LAPACK:
/Library/Frameworks/R.framework/Versions/4.0/Resources/lib/libRlapack.dylib

locale:
[1] en_CA.UTF-8/en_CA.UTF-8/en_CA.UTF-8/C/en_CA.UTF-8/en_CA.UTF-8

attached base packages:
[1] stats     graphics  grDevices utils     datasets  methods   base

other attached packages:
[1] Rmpfr_0.8-2 gmp_0.6-1

loaded via a namespace (and not attached):
[1] compiler_4.0.3


On 06/03/2021 7:07 p.m., Roger Bos wrote:

> All,
>
> The following code crashes by R on my mac with a message "R session
> aborted.  A fatal error occured".
>
> ```
> library(Rmpfr)
> Rmpfr::mpfr(pi, 120)
> ```
>
> Does anyone have any suggestions?   My session info is below:
>
> R version 4.0.3 (2020-10-10)
> Platform: x86_64-apple-darwin17.0 (64-bit)
> Running under: macOS Big Sur 10.16
>
> Matrix products: default
> LAPACK:
> /Library/Frameworks/R.framework/Versions/4.0/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] datasets  utils     stats     graphics  grDevices methods   base
>
> other attached packages:
>   [1] alphavantager_0.1.2 googlesheets4_0.2.0 googledrive_1.0.1
> clipr_0.7.1
>   [5] jsonlite_1.7.2      stringi_1.5.3       dtplyr_1.0.1
>   data.table_1.13.6
>   [9] dplyr_1.0.4         plyr_1.8.6          testthat_3.0.1
>   lubridate_1.7.9.2
> [13] timeDate_3043.102   sendmailR_1.2-1     rmarkdown_2.6
> devtools_2.3.2
> [17] usethis_2.0.0       xts_0.12.1          zoo_1.8-8
> MASS_7.3-53
> [21] fortunes_1.5-4
>
> loaded via a namespace (and not attached):
>   [1] tinytex_0.29      tidyselect_1.1.0  xfun_0.20         remotes_2.2.0
>    purrr_0.3.4
>   [6] gargle_0.5.0      lattice_0.20-41   generics_0.1.0    vctrs_0.3.6
>    htmltools_0.5.1.1
> [11] base64enc_0.1-3   rlang_0.4.10      pkgbuild_1.2.0    pillar_1.4.7
>   glue_1.4.2
> [16] withr_2.4.1       DBI_1.1.1         sessioninfo_1.1.1 lifecycle_0.2.0
>    cellranger_1.1.0
> [21] evaluate_0.14     memoise_2.0.0     knitr_1.31        callr_3.5.1
>    fastmap_1.1.0
> [26] ps_1.5.0          curl_4.3          Rcpp_1.0.6        openssl_1.4.3
>    cachem_1.0.1
> [31] desc_1.2.0        pkgload_1.1.0     fs_1.5.0          askpass_1.1
>    digest_0.6.27
> [36] processx_3.4.5    grid_4.0.3        rprojroot_2.0.2   cli_2.3.0
>    tools_4.0.3
> [41] magrittr_2.0.1    tibble_3.0.6      crayon_1.4.0      pkgconfig_2.0.3
>    ellipsis_0.3.1
> [46] prettyunits_1.1.1 httr_1.4.2        assertthat_0.2.1  R6_2.5.0
>   compiler_4.0.3
> 19:05:52  >
>
> Thanks,
>
> Roger
>
> [[alternative HTML version deleted]]
>
> ______________________________________________
> [hidden email] mailing list -- To UNSUBSCRIBE and more, see
> https://stat.ethz.ch/mailman/listinfo/r-help
> PLEASE do read the posting guide http://www.R-project.org/posting-guide.html
> and provide commented, minimal, self-contained, reproducible code.
>

______________________________________________
[hidden email] mailing list -- To UNSUBSCRIBE and more, see
https://stat.ethz.ch/mailman/listinfo/r-help
PLEASE do read the posting guide http://www.R-project.org/posting-guide.html
and provide commented, minimal, self-contained, reproducible code.
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Re: [External] Re: mpfr function in Rmpfr crashes R

Richard M. Heiberger
this is probably a Mac M1.
The problem and potential solution is described here:

https://stat.ethz.ch/pipermail/r-sig-mac/2021-February/014003.html

________________________________________
From: R-help <[hidden email]> on behalf of Duncan Murdoch <[hidden email]>
Sent: Sunday, March 7, 2021 13:03
To: Roger Bos; [hidden email]
Subject: [External] Re: [R] mpfr function in Rmpfr crashes R

It works for me, on a slightly different system than yours:

 > Rmpfr::mpfr(pi, 120)
1 'mpfr' number of precision  120   bits
[1] 3.1415926535897931159979634685441851616
 > sessionInfo()
R version 4.0.3 Patched (2021-01-30 r79912)
Platform: x86_64-apple-darwin17.0 (64-bit)
Running under: macOS Catalina 10.15.7

Matrix products: default
BLAS:
/Library/Frameworks/R.framework/Versions/4.0/Resources/lib/libRblas.dylib
LAPACK:
/Library/Frameworks/R.framework/Versions/4.0/Resources/lib/libRlapack.dylib

locale:
[1] en_CA.UTF-8/en_CA.UTF-8/en_CA.UTF-8/C/en_CA.UTF-8/en_CA.UTF-8

attached base packages:
[1] stats     graphics  grDevices utils     datasets  methods   base

other attached packages:
[1] Rmpfr_0.8-2 gmp_0.6-1

loaded via a namespace (and not attached):
[1] compiler_4.0.3


On 06/03/2021 7:07 p.m., Roger Bos wrote:

> All,
>
> The following code crashes by R on my mac with a message "R session
> aborted.  A fatal error occured".
>
> ```
> library(Rmpfr)
> Rmpfr::mpfr(pi, 120)
> ```
>
> Does anyone have any suggestions?   My session info is below:
>
> R version 4.0.3 (2020-10-10)
> Platform: x86_64-apple-darwin17.0 (64-bit)
> Running under: macOS Big Sur 10.16
>
> Matrix products: default
> LAPACK:
> /Library/Frameworks/R.framework/Versions/4.0/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] datasets  utils     stats     graphics  grDevices methods   base
>
> other attached packages:
>   [1] alphavantager_0.1.2 googlesheets4_0.2.0 googledrive_1.0.1
> clipr_0.7.1
>   [5] jsonlite_1.7.2      stringi_1.5.3       dtplyr_1.0.1
>   data.table_1.13.6
>   [9] dplyr_1.0.4         plyr_1.8.6          testthat_3.0.1
>   lubridate_1.7.9.2
> [13] timeDate_3043.102   sendmailR_1.2-1     rmarkdown_2.6
> devtools_2.3.2
> [17] usethis_2.0.0       xts_0.12.1          zoo_1.8-8
> MASS_7.3-53
> [21] fortunes_1.5-4
>
> loaded via a namespace (and not attached):
>   [1] tinytex_0.29      tidyselect_1.1.0  xfun_0.20         remotes_2.2.0
>    purrr_0.3.4
>   [6] gargle_0.5.0      lattice_0.20-41   generics_0.1.0    vctrs_0.3.6
>    htmltools_0.5.1.1
> [11] base64enc_0.1-3   rlang_0.4.10      pkgbuild_1.2.0    pillar_1.4.7
>   glue_1.4.2
> [16] withr_2.4.1       DBI_1.1.1         sessioninfo_1.1.1 lifecycle_0.2.0
>    cellranger_1.1.0
> [21] evaluate_0.14     memoise_2.0.0     knitr_1.31        callr_3.5.1
>    fastmap_1.1.0
> [26] ps_1.5.0          curl_4.3          Rcpp_1.0.6        openssl_1.4.3
>    cachem_1.0.1
> [31] desc_1.2.0        pkgload_1.1.0     fs_1.5.0          askpass_1.1
>    digest_0.6.27
> [36] processx_3.4.5    grid_4.0.3        rprojroot_2.0.2   cli_2.3.0
>    tools_4.0.3
> [41] magrittr_2.0.1    tibble_3.0.6      crayon_1.4.0      pkgconfig_2.0.3
>    ellipsis_0.3.1
> [46] prettyunits_1.1.1 httr_1.4.2        assertthat_0.2.1  R6_2.5.0
>   compiler_4.0.3
> 19:05:52  >
>
> Thanks,
>
> Roger
>
>       [[alternative HTML version deleted]]
>
> ______________________________________________
> [hidden email] mailing list -- To UNSUBSCRIBE and more, see
> https://stat.ethz.ch/mailman/listinfo/r-help
> PLEASE do read the posting guide http://www.R-project.org/posting-guide.html
> and provide commented, minimal, self-contained, reproducible code.
>

______________________________________________
[hidden email] mailing list -- To UNSUBSCRIBE and more, see
https://stat.ethz.ch/mailman/listinfo/r-help
PLEASE do read the posting guide http://www.R-project.org/posting-guide.html
and provide commented, minimal, self-contained, reproducible code.

______________________________________________
[hidden email] mailing list -- To UNSUBSCRIBE and more, see
https://stat.ethz.ch/mailman/listinfo/r-help
PLEASE do read the posting guide http://www.R-project.org/posting-guide.html
and provide commented, minimal, self-contained, reproducible code.
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Re: [External] Re: mpfr function in Rmpfr crashes R

Roger J. Bos
Richard,

Yes, I am on an M1, sorry I didn't mention it.  Sounds like I just have to
wait a bit until the problem is fixed in Rosetta2 (whatever that is).
Thanks for bringing this to my attention.

Roger


On Sun, Mar 7, 2021 at 1:33 PM Richard M. Heiberger <[hidden email]> wrote:

> this is probably a Mac M1.
> The problem and potential solution is described here:
>
> https://stat.ethz.ch/pipermail/r-sig-mac/2021-February/014003.html
>
> ________________________________________
> From: R-help <[hidden email]> on behalf of Duncan Murdoch <
> [hidden email]>
> Sent: Sunday, March 7, 2021 13:03
> To: Roger Bos; [hidden email]
> Subject: [External] Re: [R] mpfr function in Rmpfr crashes R
>
> It works for me, on a slightly different system than yours:
>
>  > Rmpfr::mpfr(pi, 120)
> 1 'mpfr' number of precision  120   bits
> [1] 3.1415926535897931159979634685441851616
>  > sessionInfo()
> R version 4.0.3 Patched (2021-01-30 r79912)
> Platform: x86_64-apple-darwin17.0 (64-bit)
> Running under: macOS Catalina 10.15.7
>
> Matrix products: default
> BLAS:
> /Library/Frameworks/R.framework/Versions/4.0/Resources/lib/libRblas.dylib
> LAPACK:
> /Library/Frameworks/R.framework/Versions/4.0/Resources/lib/libRlapack.dylib
>
> locale:
> [1] en_CA.UTF-8/en_CA.UTF-8/en_CA.UTF-8/C/en_CA.UTF-8/en_CA.UTF-8
>
> attached base packages:
> [1] stats     graphics  grDevices utils     datasets  methods   base
>
> other attached packages:
> [1] Rmpfr_0.8-2 gmp_0.6-1
>
> loaded via a namespace (and not attached):
> [1] compiler_4.0.3
>
>
> On 06/03/2021 7:07 p.m., Roger Bos wrote:
> > All,
> >
> > The following code crashes by R on my mac with a message "R session
> > aborted.  A fatal error occured".
> >
> > ```
> > library(Rmpfr)
> > Rmpfr::mpfr(pi, 120)
> > ```
> >
> > Does anyone have any suggestions?   My session info is below:
> >
> > R version 4.0.3 (2020-10-10)
> > Platform: x86_64-apple-darwin17.0 (64-bit)
> > Running under: macOS Big Sur 10.16
> >
> > Matrix products: default
> > LAPACK:
> >
> /Library/Frameworks/R.framework/Versions/4.0/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] datasets  utils     stats     graphics  grDevices methods   base
> >
> > other attached packages:
> >   [1] alphavantager_0.1.2 googlesheets4_0.2.0 googledrive_1.0.1
> > clipr_0.7.1
> >   [5] jsonlite_1.7.2      stringi_1.5.3       dtplyr_1.0.1
> >   data.table_1.13.6
> >   [9] dplyr_1.0.4         plyr_1.8.6          testthat_3.0.1
> >   lubridate_1.7.9.2
> > [13] timeDate_3043.102   sendmailR_1.2-1     rmarkdown_2.6
> > devtools_2.3.2
> > [17] usethis_2.0.0       xts_0.12.1          zoo_1.8-8
> > MASS_7.3-53
> > [21] fortunes_1.5-4
> >
> > loaded via a namespace (and not attached):
> >   [1] tinytex_0.29      tidyselect_1.1.0  xfun_0.20         remotes_2.2.0
> >    purrr_0.3.4
> >   [6] gargle_0.5.0      lattice_0.20-41   generics_0.1.0    vctrs_0.3.6
> >    htmltools_0.5.1.1
> > [11] base64enc_0.1-3   rlang_0.4.10      pkgbuild_1.2.0    pillar_1.4.7
> >   glue_1.4.2
> > [16] withr_2.4.1       DBI_1.1.1         sessioninfo_1.1.1
> lifecycle_0.2.0
> >    cellranger_1.1.0
> > [21] evaluate_0.14     memoise_2.0.0     knitr_1.31        callr_3.5.1
> >    fastmap_1.1.0
> > [26] ps_1.5.0          curl_4.3          Rcpp_1.0.6        openssl_1.4.3
> >    cachem_1.0.1
> > [31] desc_1.2.0        pkgload_1.1.0     fs_1.5.0          askpass_1.1
> >    digest_0.6.27
> > [36] processx_3.4.5    grid_4.0.3        rprojroot_2.0.2   cli_2.3.0
> >    tools_4.0.3
> > [41] magrittr_2.0.1    tibble_3.0.6      crayon_1.4.0
> pkgconfig_2.0.3
> >    ellipsis_0.3.1
> > [46] prettyunits_1.1.1 httr_1.4.2        assertthat_0.2.1  R6_2.5.0
> >   compiler_4.0.3
> > 19:05:52  >
> >
> > Thanks,
> >
> > Roger
> >
> >       [[alternative HTML version deleted]]
> >
> > ______________________________________________
> > [hidden email] mailing list -- To UNSUBSCRIBE and more, see
> > https://stat.ethz.ch/mailman/listinfo/r-help
> > PLEASE do read the posting guide
> http://www.R-project.org/posting-guide.html
> > and provide commented, minimal, self-contained, reproducible code.
> >
>
> ______________________________________________
> [hidden email] mailing list -- To UNSUBSCRIBE and more, see
> https://stat.ethz.ch/mailman/listinfo/r-help
> PLEASE do read the posting guide
> http://www.R-project.org/posting-guide.html
> and provide commented, minimal, self-contained, reproducible code.
>

        [[alternative HTML version deleted]]

______________________________________________
[hidden email] mailing list -- To UNSUBSCRIBE and more, see
https://stat.ethz.ch/mailman/listinfo/r-help
PLEASE do read the posting guide http://www.R-project.org/posting-guide.html
and provide commented, minimal, self-contained, reproducible code.