Surprising behavior and bugs in R 4.0.4

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Surprising behavior and bugs in R 4.0.4

Miso Na
Dear helpers,

Although I uninstalled and reinstalled R more than 3 times to delete the error in api_create, it did not work. The error is representing on the very first page on R consol.
Error: could not find function "api_create"

I guess this error makes impossible to install library 'SCMAP', 'SingleCellExperiment' or 'Seurat'.
For example, I got this error when I tried to install those libraries.
Installing package into 'C:/Users/user/Documents/R/win-library/4.0'
(as 'lib' is unspecified)
Error: could not find function "api_create"
Execution halted
Error: Failed to install 'Seurat' from GitHub:
  (converted from warning) installation of package 'C:/Users/user/AppData/Local/Temp/RtmpKYL3Pe/file2c2c6cb0766e/Seurat_4.0.1.tar.gz' had non-zero exit status


My sessionInfo is here!

> sessionInfo()
R version 4.0.4 (2021-02-15)
Platform: x86_64-w64-mingw32/x64 (64-bit)
Running under: Windows 10 x64 (build 19041)

Matrix products: default

locale:
[1] LC_COLLATE=English_United States.1252
[2] LC_CTYPE=English_United States.1252
[3] LC_MONETARY=English_United States.1252
[4] LC_NUMERIC=C
[5] LC_TIME=English_United States.1252
system code page: 949

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

loaded via a namespace (and not attached):
[1] compiler_4.0.4

Thanks for your help!

        [[alternative HTML version deleted]]

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Re: Surprising behavior and bugs in R 4.0.4

Duncan Murdoch-2
On 20/03/2021 1:04 a.m., Miso Na wrote:
> Dear helpers,
>
> Although I uninstalled and reinstalled R more than 3 times to delete the error in api_create, it did not work. The error is representing on the very first page on R consol.
> Error: could not find function "api_create"

Why would you think this is a bug in R, rather than in whatever
unreleased package(s) you were trying to install?

Duncan Murdoch

>
> I guess this error makes impossible to install library 'SCMAP', 'SingleCellExperiment' or 'Seurat'.
> For example, I got this error when I tried to install those libraries.
> Installing package into 'C:/Users/user/Documents/R/win-library/4.0'
> (as 'lib' is unspecified)
> Error: could not find function "api_create"
> Execution halted
> Error: Failed to install 'Seurat' from GitHub:
>    (converted from warning) installation of package 'C:/Users/user/AppData/Local/Temp/RtmpKYL3Pe/file2c2c6cb0766e/Seurat_4.0.1.tar.gz' had non-zero exit status
>
>
> My sessionInfo is here!
>
>> sessionInfo()
> R version 4.0.4 (2021-02-15)
> Platform: x86_64-w64-mingw32/x64 (64-bit)
> Running under: Windows 10 x64 (build 19041)
>
> Matrix products: default
>
> locale:
> [1] LC_COLLATE=English_United States.1252
> [2] LC_CTYPE=English_United States.1252
> [3] LC_MONETARY=English_United States.1252
> [4] LC_NUMERIC=C
> [5] LC_TIME=English_United States.1252
> system code page: 949
>
> attached base packages:
> [1] stats     graphics  grDevices utils     datasets  methods   base
>
> loaded via a namespace (and not attached):
> [1] compiler_4.0.4
>
> Thanks for your help!
>
> [[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
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Re: Surprising behavior and bugs in R 4.0.4

Jiefei Wang
In reply to this post by Miso Na
Hi Miso,

Have you tried to install Seurat from CRAN? What you were using is the
GitHub version of the package and has been actively updating, so the
problem might be from the package.

Best,
Jiefei

On Sat, Mar 20, 2021 at 10:32 PM Miso Na <[hidden email]> wrote:

> Dear helpers,
>
> Although I uninstalled and reinstalled R more than 3 times to delete the
> error in api_create, it did not work. The error is representing on the very
> first page on R consol.
> Error: could not find function "api_create"
>
> I guess this error makes impossible to install library 'SCMAP',
> 'SingleCellExperiment' or 'Seurat'.
> For example, I got this error when I tried to install those libraries.
> Installing package into 'C:/Users/user/Documents/R/win-library/4.0'
> (as 'lib' is unspecified)
> Error: could not find function "api_create"
> Execution halted
> Error: Failed to install 'Seurat' from GitHub:
>   (converted from warning) installation of package
> 'C:/Users/user/AppData/Local/Temp/RtmpKYL3Pe/file2c2c6cb0766e/Seurat_4.0.1.tar.gz'
> had non-zero exit status
>
>
> My sessionInfo is here!
>
> > sessionInfo()
> R version 4.0.4 (2021-02-15)
> Platform: x86_64-w64-mingw32/x64 (64-bit)
> Running under: Windows 10 x64 (build 19041)
>
> Matrix products: default
>
> locale:
> [1] LC_COLLATE=English_United States.1252
> [2] LC_CTYPE=English_United States.1252
> [3] LC_MONETARY=English_United States.1252
> [4] LC_NUMERIC=C
> [5] LC_TIME=English_United States.1252
> system code page: 949
>
> attached base packages:
> [1] stats     graphics  grDevices utils     datasets  methods   base
>
> loaded via a namespace (and not attached):
> [1] compiler_4.0.4
>
> Thanks for your help!
>
>         [[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.
>

        [[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.
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Re: Surprising behavior and bugs in R 4.0.4

Eric Berger
I have no familiarity with these packages but I did a search in CRAN on
api_create and found it is defined in the plotly package. I then confirmed
that the seurat package does reference plotly.

You might try installing the plotly package before trying to install seurat.

HTH,
Eric


On Sat, Mar 20, 2021 at 6:05 PM Jiefei Wang <[hidden email]> wrote:

> Hi Miso,
>
> Have you tried to install Seurat from CRAN? What you were using is the
> GitHub version of the package and has been actively updating, so the
> problem might be from the package.
>
> Best,
> Jiefei
>
> On Sat, Mar 20, 2021 at 10:32 PM Miso Na <[hidden email]> wrote:
>
> > Dear helpers,
> >
> > Although I uninstalled and reinstalled R more than 3 times to delete the
> > error in api_create, it did not work. The error is representing on the
> very
> > first page on R consol.
> > Error: could not find function "api_create"
> >
> > I guess this error makes impossible to install library 'SCMAP',
> > 'SingleCellExperiment' or 'Seurat'.
> > For example, I got this error when I tried to install those libraries.
> > Installing package into 'C:/Users/user/Documents/R/win-library/4.0'
> > (as 'lib' is unspecified)
> > Error: could not find function "api_create"
> > Execution halted
> > Error: Failed to install 'Seurat' from GitHub:
> >   (converted from warning) installation of package
> >
> 'C:/Users/user/AppData/Local/Temp/RtmpKYL3Pe/file2c2c6cb0766e/Seurat_4.0.1.tar.gz'
> > had non-zero exit status
> >
> >
> > My sessionInfo is here!
> >
> > > sessionInfo()
> > R version 4.0.4 (2021-02-15)
> > Platform: x86_64-w64-mingw32/x64 (64-bit)
> > Running under: Windows 10 x64 (build 19041)
> >
> > Matrix products: default
> >
> > locale:
> > [1] LC_COLLATE=English_United States.1252
> > [2] LC_CTYPE=English_United States.1252
> > [3] LC_MONETARY=English_United States.1252
> > [4] LC_NUMERIC=C
> > [5] LC_TIME=English_United States.1252
> > system code page: 949
> >
> > attached base packages:
> > [1] stats     graphics  grDevices utils     datasets  methods   base
> >
> > loaded via a namespace (and not attached):
> > [1] compiler_4.0.4
> >
> > Thanks for your help!
> >
> >         [[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.
> >
>
>         [[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.
>

        [[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.
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Re: Surprising behavior and bugs in R 4.0.4

Jiefei Wang
In reply to this post by Jiefei Wang
Hi Miso,

It looks like you have a corrupted package library, probably due to some
packages installed from an unofficial repository(e.g. GitHub). I will
suggest first installing the package "spatstat"(This is the package that
should define "markvario"), then try to install "Seurat" again and see if
it works.

If it doesn't work. Please remove all folders under the path shown in
".libPaths()" and reinstall your R, then installing "Seurat" from CRAN
should work.

Best,
Jiefei

On Sun, Mar 21, 2021 at 2:05 AM Miso Na <[hidden email]> wrote:

> Thanks for your reply!
>
> Seurat was downloaded from CRAN, with the below code.
>
> > install.packages('Seurat')
>
>
>
> It seems to work, but when I use as library, the error shows up!
>
> > library(Seurat)
>
> Error: package or namespace load failed for ‘Seurat’:
>
> object ‘markvario’ is not exported by 'namespace:spatstat'
>
>
>
> And of course, I tried to download packages ‘markvario’, but
>
>
>
> > install.packages('markvario')
>
> Installing package into ‘C:/Users/user/Documents/R/win-library/4.0’
>
> (as ‘lib’ is unspecified)
>
> Warning message:
>
> package ‘markvario’ is not available for this version of R
>
>
>
> A version of this package for your version of R might be available
> elsewhere,
>
> see the ideas at
>
>
> https://cran.r-project.org/doc/manuals/r-patched/R-admin.html#Installing-packages
>
> > install.packages('
> https://cran.r-project.org/src/contrib/Archive/spatstat/spatstat_1.64-1.tar.gz',
> repos=NULL,type="source", INSTALL_opts = "--no-lock")
>
> Installing package into ‘C:/Users/user/Documents/R/win-library/4.0’
>
> (as ‘lib’ is unspecified)
>
> trying URL '
> https://cran.r-project.org/src/contrib/Archive/spatstat/spatstat_1.64-1.tar.gz
> '
>
> Content type 'application/x-gzip' length 7943393 bytes (7.6 MB)
>
> downloaded 7.6 MB
>
>
>
> Error: could not find function "api_create"
>
> Execution halted
>
> Warning message:
>
> In install.packages(
> https://cran.r-project.org/src/contrib/Archive/spatstat/spatstat_1.64-1.tar.gz,
> :
>
>   installation of package
> ‘C:/Users/user/AppData/Local/Temp/RtmpWmLFdn/downloaded_packages/spatstat_1.64-1.tar.gz’
> had non-zero exit status
>
>
>
> Thanks,
>
> Miso
>
> *From:* Jiefei Wang <[hidden email]>
> *Sent:* Sunday, March 21, 2021 1:05 AM
> *To:* Miso Na <[hidden email]>
> *Cc:* [hidden email]; Ray Cheng <[hidden email]>; Patrick Cahan <
> [hidden email]>
> *Subject:* Re: [R] Surprising behavior and bugs in R 4.0.4
>
>
>
>
> *      External Email - Use Caution      *
>
>
>
>
>
> Hi Miso,
>
>
>
> Have you tried to install Seurat from CRAN? What you were using is the
> GitHub version of the package and has been actively updating, so the
> problem might be from the package.
>
>
>
> Best,
>
> Jiefei
>
>
>
> On Sat, Mar 20, 2021 at 10:32 PM Miso Na <[hidden email]> wrote:
>
> Dear helpers,
>
> Although I uninstalled and reinstalled R more than 3 times to delete the
> error in api_create, it did not work. The error is representing on the very
> first page on R consol.
> Error: could not find function "api_create"
>
> I guess this error makes impossible to install library 'SCMAP',
> 'SingleCellExperiment' or 'Seurat'.
> For example, I got this error when I tried to install those libraries.
> Installing package into 'C:/Users/user/Documents/R/win-library/4.0'
> (as 'lib' is unspecified)
> Error: could not find function "api_create"
> Execution halted
> Error: Failed to install 'Seurat' from GitHub:
>   (converted from warning) installation of package
> 'C:/Users/user/AppData/Local/Temp/RtmpKYL3Pe/file2c2c6cb0766e/Seurat_4.0.1.tar.gz'
> had non-zero exit status
>
>
> My sessionInfo is here!
>
> > sessionInfo()
> R version 4.0.4 (2021-02-15)
> Platform: x86_64-w64-mingw32/x64 (64-bit)
> Running under: Windows 10 x64 (build 19041)
>
> Matrix products: default
>
> locale:
> [1] LC_COLLATE=English_United States.1252
> [2] LC_CTYPE=English_United States.1252
> [3] LC_MONETARY=English_United States.1252
> [4] LC_NUMERIC=C
> [5] LC_TIME=English_United States.1252
> system code page: 949
>
> attached base packages:
> [1] stats     graphics  grDevices utils     datasets  methods   base
>
> loaded via a namespace (and not attached):
> [1] compiler_4.0.4
>
> Thanks for your help!
>
>         [[alternative HTML version deleted]]
>
> ______________________________________________
> [hidden email] mailing list -- To UNSUBSCRIBE and more, see
> https://stat.ethz.ch/mailman/listinfo/r-help
> <https://nam02.safelinks.protection.outlook.com/?url=https%3A%2F%2Fstat.ethz.ch%2Fmailman%2Flistinfo%2Fr-help&data=04%7C01%7Cmna3%40jhu.edu%7Ccb5c11919a794eb1768208d8ebb9e4d4%7C9fa4f438b1e6473b803f86f8aedf0dec%7C0%7C0%7C637518531387699796%7CUnknown%7CTWFpbGZsb3d8eyJWIjoiMC4wLjAwMDAiLCJQIjoiV2luMzIiLCJBTiI6Ik1haWwiLCJXVCI6Mn0%3D%7C2000&sdata=eJCLhgeiwB2zy6IYHc3%2Be9Hc8kHYUOiCPbssMg8PBRg%3D&reserved=0>
> PLEASE do read the posting guide
> http://www.R-project.org/posting-guide.html
> <https://nam02.safelinks.protection.outlook.com/?url=http%3A%2F%2Fwww.r-project.org%2Fposting-guide.html&data=04%7C01%7Cmna3%40jhu.edu%7Ccb5c11919a794eb1768208d8ebb9e4d4%7C9fa4f438b1e6473b803f86f8aedf0dec%7C0%7C0%7C637518531387709792%7CUnknown%7CTWFpbGZsb3d8eyJWIjoiMC4wLjAwMDAiLCJQIjoiV2luMzIiLCJBTiI6Ik1haWwiLCJXVCI6Mn0%3D%7C2000&sdata=KMjEPl4zrYrj9awZNxr%2FLbgMvAGFAX%2FKZ5I9gd6P0IY%3D&reserved=0>
> 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.
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Re: Surprising behavior and bugs in R 4.0.4

Jiefei Wang
FYI, you do not have to provide a full link to the function
"install.packages". Please install the package just by
install.package("package name")

Best,
Jiefei

On Sun, Mar 21, 2021 at 9:41 AM Jiefei Wang <[hidden email]> wrote:

> Hi Miso,
>
> It looks like you have a corrupted package library, probably due to some
> packages installed from an unofficial repository(e.g. GitHub). I will
> suggest first installing the package "spatstat"(This is the package that
> should define "markvario"), then try to install "Seurat" again and see if
> it works.
>
> If it doesn't work. Please remove all folders under the path shown in
> ".libPaths()" and reinstall your R, then installing "Seurat" from CRAN
> should work.
>
> Best,
> Jiefei
>
> On Sun, Mar 21, 2021 at 2:05 AM Miso Na <[hidden email]> wrote:
>
>> Thanks for your reply!
>>
>> Seurat was downloaded from CRAN, with the below code.
>>
>> > install.packages('Seurat')
>>
>>
>>
>> It seems to work, but when I use as library, the error shows up!
>>
>> > library(Seurat)
>>
>> Error: package or namespace load failed for ‘Seurat’:
>>
>> object ‘markvario’ is not exported by 'namespace:spatstat'
>>
>>
>>
>> And of course, I tried to download packages ‘markvario’, but
>>
>>
>>
>> > install.packages('markvario')
>>
>> Installing package into ‘C:/Users/user/Documents/R/win-library/4.0’
>>
>> (as ‘lib’ is unspecified)
>>
>> Warning message:
>>
>> package ‘markvario’ is not available for this version of R
>>
>>
>>
>> A version of this package for your version of R might be available
>> elsewhere,
>>
>> see the ideas at
>>
>>
>> https://cran.r-project.org/doc/manuals/r-patched/R-admin.html#Installing-packages
>>
>> > install.packages('
>> https://cran.r-project.org/src/contrib/Archive/spatstat/spatstat_1.64-1.tar.gz',
>> repos=NULL,type="source", INSTALL_opts = "--no-lock")
>>
>> Installing package into ‘C:/Users/user/Documents/R/win-library/4.0’
>>
>> (as ‘lib’ is unspecified)
>>
>> trying URL '
>> https://cran.r-project.org/src/contrib/Archive/spatstat/spatstat_1.64-1.tar.gz
>> '
>>
>> Content type 'application/x-gzip' length 7943393 bytes (7.6 MB)
>>
>> downloaded 7.6 MB
>>
>>
>>
>> Error: could not find function "api_create"
>>
>> Execution halted
>>
>> Warning message:
>>
>> In install.packages(
>> https://cran.r-project.org/src/contrib/Archive/spatstat/spatstat_1.64-1.tar.gz,
>> :
>>
>>   installation of package
>> ‘C:/Users/user/AppData/Local/Temp/RtmpWmLFdn/downloaded_packages/spatstat_1.64-1.tar.gz’
>> had non-zero exit status
>>
>>
>>
>> Thanks,
>>
>> Miso
>>
>> *From:* Jiefei Wang <[hidden email]>
>> *Sent:* Sunday, March 21, 2021 1:05 AM
>> *To:* Miso Na <[hidden email]>
>> *Cc:* [hidden email]; Ray Cheng <[hidden email]>; Patrick Cahan
>> <[hidden email]>
>> *Subject:* Re: [R] Surprising behavior and bugs in R 4.0.4
>>
>>
>>
>>
>> *      External Email - Use Caution      *
>>
>>
>>
>>
>>
>> Hi Miso,
>>
>>
>>
>> Have you tried to install Seurat from CRAN? What you were using is the
>> GitHub version of the package and has been actively updating, so the
>> problem might be from the package.
>>
>>
>>
>> Best,
>>
>> Jiefei
>>
>>
>>
>> On Sat, Mar 20, 2021 at 10:32 PM Miso Na <[hidden email]> wrote:
>>
>> Dear helpers,
>>
>> Although I uninstalled and reinstalled R more than 3 times to delete the
>> error in api_create, it did not work. The error is representing on the very
>> first page on R consol.
>> Error: could not find function "api_create"
>>
>> I guess this error makes impossible to install library 'SCMAP',
>> 'SingleCellExperiment' or 'Seurat'.
>> For example, I got this error when I tried to install those libraries.
>> Installing package into 'C:/Users/user/Documents/R/win-library/4.0'
>> (as 'lib' is unspecified)
>> Error: could not find function "api_create"
>> Execution halted
>> Error: Failed to install 'Seurat' from GitHub:
>>   (converted from warning) installation of package
>> 'C:/Users/user/AppData/Local/Temp/RtmpKYL3Pe/file2c2c6cb0766e/Seurat_4.0.1.tar.gz'
>> had non-zero exit status
>>
>>
>> My sessionInfo is here!
>>
>> > sessionInfo()
>> R version 4.0.4 (2021-02-15)
>> Platform: x86_64-w64-mingw32/x64 (64-bit)
>> Running under: Windows 10 x64 (build 19041)
>>
>> Matrix products: default
>>
>> locale:
>> [1] LC_COLLATE=English_United States.1252
>> [2] LC_CTYPE=English_United States.1252
>> [3] LC_MONETARY=English_United States.1252
>> [4] LC_NUMERIC=C
>> [5] LC_TIME=English_United States.1252
>> system code page: 949
>>
>> attached base packages:
>> [1] stats     graphics  grDevices utils     datasets  methods   base
>>
>> loaded via a namespace (and not attached):
>> [1] compiler_4.0.4
>>
>> Thanks for your help!
>>
>>         [[alternative HTML version deleted]]
>>
>> ______________________________________________
>> [hidden email] mailing list -- To UNSUBSCRIBE and more, see
>> https://stat.ethz.ch/mailman/listinfo/r-help
>> <https://nam02.safelinks.protection.outlook.com/?url=https%3A%2F%2Fstat.ethz.ch%2Fmailman%2Flistinfo%2Fr-help&data=04%7C01%7Cmna3%40jhu.edu%7Ccb5c11919a794eb1768208d8ebb9e4d4%7C9fa4f438b1e6473b803f86f8aedf0dec%7C0%7C0%7C637518531387699796%7CUnknown%7CTWFpbGZsb3d8eyJWIjoiMC4wLjAwMDAiLCJQIjoiV2luMzIiLCJBTiI6Ik1haWwiLCJXVCI6Mn0%3D%7C2000&sdata=eJCLhgeiwB2zy6IYHc3%2Be9Hc8kHYUOiCPbssMg8PBRg%3D&reserved=0>
>> PLEASE do read the posting guide
>> http://www.R-project.org/posting-guide.html
>> <https://nam02.safelinks.protection.outlook.com/?url=http%3A%2F%2Fwww.r-project.org%2Fposting-guide.html&data=04%7C01%7Cmna3%40jhu.edu%7Ccb5c11919a794eb1768208d8ebb9e4d4%7C9fa4f438b1e6473b803f86f8aedf0dec%7C0%7C0%7C637518531387709792%7CUnknown%7CTWFpbGZsb3d8eyJWIjoiMC4wLjAwMDAiLCJQIjoiV2luMzIiLCJBTiI6Ik1haWwiLCJXVCI6Mn0%3D%7C2000&sdata=KMjEPl4zrYrj9awZNxr%2FLbgMvAGFAX%2FKZ5I9gd6P0IY%3D&reserved=0>
>> and provide commented, minimal, self-contained, reproducible code.
>>
>>

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PLEASE do read the posting guide http://www.R-project.org/posting-guide.html
and provide commented, minimal, self-contained, reproducible code.