[R-pkg-devel] Assistance Needed to Resolve CRAN Submission Note

Thu May 16 18:09:59 CEST 2024

Zeinab

I have found that setting this system value to FALSE eliminates the issue:

Sys.setenv("_R_CHECK_RD_VALIDATE_RD2HTML_" = FALSE)

- Keith

On 5/16/24, 12:02 PM, "R-package-devel on behalf of Zeinab Mashreghi" <r-package-devel-bounces using r-project.org <mailto:r-package-devel-bounces using r-project.org> on behalf of z.mashreghi using uwinnipeg.ca <mailto:z.mashreghi using uwinnipeg.ca>> wrote:

[EXTERNAL]

Hi,

Thank you very much for your helpful suggestion! Following your advice, I revisited the package and made necessary adjustments to the description file. However, it appears that there are now some issues with HTML validation in the .Rd files. Here's the relevant excerpt, and I've attached the log for further reference.

checking HTML version of manual ... NOTE
Found the following HTML validation problems:
All.data.html:4:1 (All.data.Rd:10): Warning: <link> inserting "type" attribute
All.data.html:12:1 (All.data.Rd:10): Warning: <script> proprietary attribute "onload"
All.data.html:12:1 (All.data.Rd:10): Warning: <script> inserting "type" attribute
All.data.html:17:1 (All.data.Rd:10): Warning: <table> lacks "summary" attribute
All.data.html:19:1 (All.data.Rd:10): Warning: <h2> attribute "id" has invalid value

Thank you for your ongoing support!

Best regards,

Zeinab

From: Ivan Krylov <ikrylov using disroot.org <mailto:ikrylov using disroot.org>>
Date: Thursday, May 16, 2024 at 4:07 AM
To: Zeinab Mashreghi <z.mashreghi using uwinnipeg.ca <mailto:z.mashreghi using uwinnipeg.ca>>
Cc: r-package-devel using r-project.org <mailto:r-package-devel using r-project.org> <r-package-devel using r-project.org <mailto:r-package-devel using r-project.org>>
Subject: Re: [R-pkg-devel] Assistance Needed to Resolve CRAN Submission Note
Notice: This is external email. Verify the sender and use caution with any content.

Dear Zeinab,

Welcome to R-package-devel!

В Thu, 16 May 2024 03:22:56 +0000
Zeinab Mashreghi <z.mashreghi using uwinnipeg.ca <mailto:z.mashreghi using uwinnipeg.ca>> пишет:

> I recently submitted my R package to CRAN, and I received this note
> from the CRAN teams: "checking CRAN incoming feasibility ... NOTE."

Without a link to the full error log and, ideally, to the source code
of the package, it's impossible to help with such a NOTE, because the
check for "CRAN incoming feasibility" encompasses many tests. I was
lucky to fish your package from the archived queue and correlate it
with the publicly available logs, but it's not always this simple:

https://win-builder.r-project.org/incoming_pretest/bootsurv_0.0.0.9000_20240515_212834/ <https://win-builder.r-project.org/incoming_pretest/bootsurv_0.0.0.9000_20240515_212834/>

>> New submission

This is expected and will always result in a NOTE to flag the package
to a CRAN reviewer.

>> Version contains large components (0.0.0.9000)

The convention is to use version components like 9000 for pre-release,
untested versions of packages. Could you please use a version like
0.0.1 for the version of the package to be released on CRAN?

> Unknown, possibly misspelled, fields in DESCRIPTION:
> ‘ImportFrom’ ‘Data’

'importFrom' is a NAMESPACE file directive [1]. The DESCRIPTION must
list 'Imports:' instead [2]. What did you intend to mean with the Data:
field of your DESCRIPTION?

>> The Title field should be in title case. Current version is:
>> ‘Bootstrap Methods for complete (absence of missing values) survey
>> data’
>> In title case that is:
>> ‘Bootstrap Methods for Complete (Absence of Missing Values) Survey
>> Data’

This is yet another CRAN convention. You'll need to change the 'Title:'
field of the DESCRIPTION file.

>> * checking Rd line widths ... NOTE
>> Rd file 'boot.twostage.Rd':
>> \examples lines wider than 100 characters:

Could you please wrap the lines of your \examples{} sections to 100
characters or less?

>> * checking examples ... [21m/21m] NOTE
>> Examples with CPU (user + system) or elapsed time > 5s
>> user system elapsed
>> boot.weights.stsrs 1242.735 0.492 1243.285
>> boot.twostage 9.799 0.048 9.847

The \examples{...} in your documentation are not only to be read by the
user. R CMD check runs them periodically on the CRAN servers. The user
should also be able to run example(boot.weights.stsrs) and see your
code directly in action. CRAN requires examples to run in 5 seconds or
less, both elapsed and CPU time. An example(...) that runs for 20
minutes is way too long. You'll need to find a way to reduce the time
spent in the example.

Wasn't something like this said in the e-mail you received from CRAN?

> When I run R CMD check on my device, I do not encounter any issues,

Even with R CMD check --as-cran?

--
Best regards,
Ivan

[1]
https://cran.r-project.org/doc/manuals/R-exts.html#Specifying-imports-and-exports <https://cran.r-project.org/doc/manuals/R-exts.html#Specifying-imports-and-exports>

[2]
https://cran.r-project.org/doc/manuals/R-exts.html#The-DESCRIPTION-file <https://cran.r-project.org/doc/manuals/R-exts.html#The-DESCRIPTION-file>
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