Re: [Rd] Issue with data() function
Duncan and others: I was not being careful with my description. This
concerned tests of
version 3.2-8, not yet on CRAN, in which I was trying some size-limiting
measures. My
apologies for not making this clear.
- I feel mild pressure to make the survival package smaller, per CRAN
guidelines, and
shrinking the data appears to be one way to approach that. So a real point of
the query
is my attempts to do so. (I am much more resistant to shrinking the extensive
test suite
or the vignettes.)
- The survival package has a lot of small data sets, and bundling them up
into a
single .rda file does save space, but it causes some issues with data(). The
overall
tarball goes from 7480 to 6100 in size (ls -s).
Terry
On 10/24/20 4:28 AM, Duncan Murdoch wrote:
> On 23/10/2020 9:25 p.m., Therneau, Terry M., Ph.D. via R-devel wrote:
>> I found an issue with the data() command this evening when working on the
>> survival
>> package.
>>
>> 1. I have a lot of data sets in the package, almost all used in at least one
>> vignette,
>> help file, or test. As a space saving measure, I have bundled many of them
>> together,
>> i.e., the file data/cancer.rda contains 19 data sets, many of them small.
>> The resulting
>> file (using xz compression) is quite a bit smaller than the individual ones.
>> (I still get
>> a warning note about size from R CMD check, but I'm no longer 2x the limit.)
>>
>> 2. Consider the lung data set. All of these fail:
>> data(lung)
>> data("lung")
>> data(lung, package="survival")
>>
>> a. The lung.Rd file had \usage{data(lung)}; that error was not caught by
>> R CMD check.
>> (Several other .Rd files as well.)
>>
>> b. In broader examples for teaching, I sometimes load data from other
>> packages, e.g
>> data(aidssi, package="mstate"). But this does not work for survival. (The
>> larger
>> survival data sets that are in separate .rda files can be found.)
>>
>> c. What does work is survival::lung. Might it be useful to add a comment
>> to data.Rd to
>> this effect?
>
> You don't describe how this dataset is being included in your package. Have
> you moved it
> from data/lung.rda to data/cancer.rda? Currently (in survival 3.2-7) each of
> these works
> for me:
>
> library(survival); data(lung)
>
> library(survival); data("lung")
>
> # Without library(survival):
> data(lung, package="survival")
>
> I think if the lung dataset is now being included in cancer.rda, you'd need
>
> data(cancer, package="survival")
>
> or equivalent to load it (and the rest of the datasets there).
>
>>
>>
>> 3. Creating a separate package 'survivaldata' is of course one route, and is
>> suggested in
>> the "Writing R Extensions" guide. But this is not possible since survival
>> is a
>> recommended package: it can't load any non-recommended package for it's
>> tests or
>> vignettes. Longer term, perhaps there is way around this constraint?
>
> Maybe the solution is to put your datasets into the "datasets" package, or
> make
> "survivaldata" a recommended package, or just leave things as they are and
> ignore the
> warnings about package size. I think that's a negotiation you should have
> with R Core.
>
> Duncan Murdoch
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Re: [Rd] Issue with data() function
On 24/10/2020 2:00 p.m., Dirk Eddelbuettel wrote: On 24 October 2020 at 05:28, Duncan Murdoch wrote: | they are and ignore the warnings about package size. I think that's a | negotiation you should have with R Core. s/R Core/CRAN/ ? Yes, for that part. The other suggestions need R Core agreement. Duncan Murdoch __ R-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-devel
Re: [Rd] Issue with data() function
On 24 October 2020 at 05:28, Duncan Murdoch wrote: | they are and ignore the warnings about package size. I think that's a | negotiation you should have with R Core. s/R Core/CRAN/ ? Dirk -- https://dirk.eddelbuettel.com | @eddelbuettel | e...@debian.org __ R-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-devel
Re: [Rd] Issue with data() function
On 23/10/2020 9:25 p.m., Therneau, Terry M., Ph.D. via R-devel wrote:
I found an issue with the data() command this evening when working on the
survival package.
1. I have a lot of data sets in the package, almost all used in at least one
vignette,
help file, or test. As a space saving measure, I have bundled many of them
together,
i.e., the file data/cancer.rda contains 19 data sets, many of them small. The
resulting
file (using xz compression) is quite a bit smaller than the individual ones.
(I still get
a warning note about size from R CMD check, but I'm no longer 2x the limit.)
2. Consider the lung data set. All of these fail:
data(lung)
data("lung")
data(lung, package="survival")
a. The lung.Rd file had \usage{data(lung)}; that error was not caught by R
CMD check.
(Several other .Rd files as well.)
b. In broader examples for teaching, I sometimes load data from other
packages, e.g
data(aidssi, package="mstate"). But this does not work for survival. (The
larger
survival data sets that are in separate .rda files can be found.)
c. What does work is survival::lung. Might it be useful to add a comment to
data.Rd to
this effect?
You don't describe how this dataset is being included in your package.
Have you moved it from data/lung.rda to data/cancer.rda? Currently (in
survival 3.2-7) each of these works for me:
library(survival); data(lung)
library(survival); data("lung")
# Without library(survival):
data(lung, package="survival")
I think if the lung dataset is now being included in cancer.rda, you'd need
data(cancer, package="survival")
or equivalent to load it (and the rest of the datasets there).
3. Creating a separate package 'survivaldata' is of course one route, and is
suggested in
the "Writing R Extensions" guide. But this is not possible since survival is a
recommended package: it can't load any non-recommended package for it's tests or
vignettes. Longer term, perhaps there is way around this constraint?
Maybe the solution is to put your datasets into the "datasets" package,
or make "survivaldata" a recommended package, or just leave things as
they are and ignore the warnings about package size. I think that's a
negotiation you should have with R Core.
Duncan Murdoch
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[Rd] Issue with data() function
I found an issue with the data() command this evening when working on the
survival package.
1. I have a lot of data sets in the package, almost all used in at least one
vignette,
help file, or test. As a space saving measure, I have bundled many of them
together,
i.e., the file data/cancer.rda contains 19 data sets, many of them small. The
resulting
file (using xz compression) is quite a bit smaller than the individual ones.
(I still get
a warning note about size from R CMD check, but I'm no longer 2x the limit.)
2. Consider the lung data set. All of these fail:
data(lung)
data("lung")
data(lung, package="survival")
a. The lung.Rd file had \usage{data(lung)}; that error was not caught by R
CMD check.
(Several other .Rd files as well.)
b. In broader examples for teaching, I sometimes load data from other
packages, e.g
data(aidssi, package="mstate"). But this does not work for survival. (The
larger
survival data sets that are in separate .rda files can be found.)
c. What does work is survival::lung. Might it be useful to add a comment to
data.Rd to
this effect?
3. Creating a separate package 'survivaldata' is of course one route, and is
suggested in
the "Writing R Extensions" guide. But this is not possible since survival is a
recommended package: it can't load any non-recommended package for it's tests
or
vignettes. Longer term, perhaps there is way around this constraint?
Terry T.
--
Terry M Therneau, PhD
Department of Health Science Research
Mayo Clinic
thern...@mayo.edu
"TERR-ree THUR-noh"
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