issue with data()

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issue with data()

R devel mailing list
I am testing out the next release of survival, which involves running R CMD check on 868
CRAN packages that import, depend or suggest it.

The survival package has a lot of data sets, most of which are non-trivial real examples
(something I'm proud of).  To save space I've bundled many of them, .e.g., data/cancer.rda
has 19 different dataframes.

This caused failures in 4 packages, each because they have a line such as "data(lung)"  or
data(breast, package= "survival"); and the data() command looks for a file name.

This is a question about which option is considered the best (perhaps more of a poll),
between two choices

1. unbundle them again  (it does save 1/3 of the space, and I do get complaints from R CMD
build about size)
2. send notes to the 4 maintainers.  The help files for the data sets have the usage
documented as  "lung" or "breast", and not data(lung), so I am technically legal to claim
they have a mistake.

A third option to make the data sets a separate package is not on the table.  I use them
heavily in my help files and test suite, and since survival is a recommended package I
can't add library(x) statements for  !(x %in% recommended).   I am guessing that this
would also break many dependent packages.

Terry T.

--
Terry M Therneau, PhD
Department of Health Science Research
Mayo Clinic
[hidden email]

"TERR-ree THUR-noh"


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Re: issue with data()

Michael Dewey-3
Dear Terry

Option 2 looks the best to me. They have a relatively simple change to
make and there are only four of them.

Michael

On 16/02/2021 14:39, Therneau, Terry M., Ph.D. via R-devel wrote:

> I am testing out the next release of survival, which involves running R CMD check on 868
> CRAN packages that import, depend or suggest it.
>
> The survival package has a lot of data sets, most of which are non-trivial real examples
> (something I'm proud of).  To save space I've bundled many of them, .e.g., data/cancer.rda
> has 19 different dataframes.
>
> This caused failures in 4 packages, each because they have a line such as "data(lung)"  or
> data(breast, package= "survival"); and the data() command looks for a file name.
>
> This is a question about which option is considered the best (perhaps more of a poll),
> between two choices
>
> 1. unbundle them again  (it does save 1/3 of the space, and I do get complaints from R CMD
> build about size)
> 2. send notes to the 4 maintainers.  The help files for the data sets have the usage
> documented as  "lung" or "breast", and not data(lung), so I am technically legal to claim
> they have a mistake.
>
> A third option to make the data sets a separate package is not on the table.  I use them
> heavily in my help files and test suite, and since survival is a recommended package I
> can't add library(x) statements for  !(x %in% recommended).   I am guessing that this
> would also break many dependent packages.
>
> Terry T.
>

--
Michael
http://www.dewey.myzen.co.uk/home.html

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Re: issue with data()

David Scott-6
In reply to this post by R devel mailing list
I would recommend option 2. I have done that when changes to xtable broke some packages. xtable has a number of dependencies but not on the scale of survival. Just 4 packages out of 868 seems minimal to me.

David Scott

On 17/02/2021 3:39 am, Therneau, Terry M., Ph.D. via R-devel wrote:
I am testing out the next release of survival, which involves running R CMD check on 868
CRAN packages that import, depend or suggest it.

The survival package has a lot of data sets, most of which are non-trivial real examples
(something I'm proud of).  To save space I've bundled many of them, .e.g., data/cancer.rda
has 19 different dataframes.

This caused failures in 4 packages, each because they have a line such as "data(lung)"  or
data(breast, package= "survival"); and the data() command looks for a file name.

This is a question about which option is considered the best (perhaps more of a poll),
between two choices

1. unbundle them again  (it does save 1/3 of the space, and I do get complaints from R CMD
build about size)
2. send notes to the 4 maintainers.  The help files for the data sets have the usage
documented as  "lung" or "breast", and not data(lung), so I am technically legal to claim
they have a mistake.

A third option to make the data sets a separate package is not on the table.  I use them
heavily in my help files and test suite, and since survival is a recommended package I
can't add library(x) statements for  !(x %in% recommended).   I am guessing that this
would also break many dependent packages.

Terry T.

--
Terry M Therneau, PhD
Department of Health Science Research
Mayo Clinic
[hidden email]<mailto:[hidden email]>

"TERR-ree THUR-noh"


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--
_________________________________________________________________
David Scott
Department of Statistics
The University of Auckland, PB 92019
Auckland 1142,    NEW ZEALAND
Email:    [hidden email]<mailto:[hidden email]>

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